{"action":"created","comment":{"url":"https://api.github.com/repos/ARTbio/tools-artbio/pulls/comments/233953528","pull_request_review_id":175478219,"id":233953528,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDIzMzk1MzUyOA==","diff_hunk":"@@ -0,0 +1,270 @@\n+<tool id=\"filter_cells_and_genes\" name=\"Filter out cells and genes\" version=\"0.1.0\">\n+  <description>from raw counts single cell RNAseq expression values\"</description>\n+  <requirements>\n+      <requirement type=\"package\" version=\"2.3.1=r3.4.1_0\">r-seurat</requirement>\n+      <requirement type=\"package\" version=\"1.6.0=r3.4.1_0\">bioconductor-scater</requirement>\n+      <requirement type=\"package\" version=\"1.0.0=r3.4.1_0\">bioconductor-singlecellexperiment</requirement>\n+      <requirement type=\"package\" version=\"1.6.0=r341_0\">r-optparse</requirement>\n+   </requirements>\n+   <stdio>\n+      <exit_code range=\"1:\" level=\"fatal\" description=\"Tool exception\" />\n+   </stdio>\n+   <command detect_errors=\"exit_code\"><![CDATA[\n+\n+Rscript $__tool_directory__/filter_cells_and_genes.R\n+    -f $file\n+    -c $file_header\n+    -s $file_sep\n+    -m $option.is_mito\n+    #if $option.is_mito == \"TRUE\":\n+        --header_mito $option.header_mito\n+    #end if\n+    -p $method.package\n+    #if $method.package == \"scater\":\n+        -g $method.feature_removing.gene_filter\n+        #if $method.feature_removing.gene_filter == \"low.abundances\":\n+            --min_cells $method.feature_removing.min_counts\n+        #end if\n+        #if $method.feature_removing.gene_filter == \"min.cells\":\n+            --min_cells $method.feature_removing.min_cells\n+        #end if\n+    #end if\n+    #if $method.package == \"Seurat\":\n+        --min_genes $method.min_genes\n+        --min_cells $method.min_cells\n+    #end if\n+    --output_pdf $output_plot\n+    --output_matrix $output_matrix\n+\n+]]></command>\n+   <inputs>\n+      <param name=\"file\" type=\"data\" format=\"txt\" label=\"Raw counts of expression data\"/>\n+      <param name=\"file_sep\" type=\"select\" label=\"Input column separator\">\n+         <option value=\"tab\" selected=\"true\">Tabs</option>\n+         <option value=\",\">Commas</option>\n+         <option value=\" \">Whitespaces</option>\n+         <option value=\".\">Dots</option>\n+         <option value=\"_\">Underscores</option>\n+         <option value=\"-\">Dashes</option>\n+   </param>\n+   <param name=\"file_header\" type=\"select\" label=\"Consider first line of input file as header?\">\n+      <option value=\"TRUE\" selected=\"true\">Yes</option>\n+      <option value=\"FALSE\">No</option>\n+   </param>\n+   <conditional name=\"option\">\n+      <param name=\"is_mito\" type=\"select\" label=\"Do you want to remove cells that detect more than 20% of mitochondrial genes ? (only applicable if mitochondrial genes are in the expression data)\">\n+         <option value=\"FALSE\" selected=\"true\">No</option>\n+         <option value=\"TRUE\">Yes</option>\n+      </param>\n+      <when value=\"TRUE\">\n+         <param name=\"header_mito\" type=\"text\" label=\"Regular expression for selection of mitochondrial genes\"/>\n+      </when>\n+      <when value=\"FALSE\">\n+      </when>\n+   </conditional>\n+   <conditional name=\"method\">\n+      <param name=\"package\" type=\"select\" label=\"Which package/method do you want to use ?\">\n+         <option value=\"scater\" selected=\"true\">scater</option>\n+         <option value=\"Seurat\">Seurat</option>\n+      </param>\n+      <when value=\"scater\">\n+         <conditional name=\"feature_removing\">\n+            <param name=\"gene_filter\" type=\"select\" label=\"How do you want to filter out genes ?\">\n+               <option value=\"low.abundances\" selected=\"true\">low abundances genes relative to library size</option>\n+               <option value=\"min.cells\">genes that aren't detected in a fraction of cells</option>\n+            </param>\n+            <when value=\"low.abundances\">\n+               <param name=\"min_counts\" type=\"integer\" value=\"1\" label=\"Keep all genes with an average count equal or higher than:\"/>\n+            </when>\n+            <when value=\"min.cells\">\n+               <param name=\"min_cells\" type=\"integer\" value=\"3\" label=\"Keep all genes that are detected in at least n cells:\"/>\n+            </when>\n+        </conditional>\n+      </when>\n+      <when value=\"Seurat\">\n+         <param name=\"min_genes\" type=\"integer\" value=\"5\" label=\"Keep all cells that detect at least n genes:\"/>\n+         <param name=\"min_cells\" type=\"integer\" value=\"3\" label=\"Keep all genes that are detected in at least n cells:\"/>\n+      </when>\n+   </conditional>\n+   </inputs>\n+   <outputs>\n+         <data name=\"output_plot\" format=\"pdf\" label=\"PDF plots from ${on_string}\"/>\n+         <data name=\"output_matrix\" format=\"tabular\" label=\"Filtered expression matrix from ${on_string}\"/>\n+   </outputs>\n+   <tests>\n+      <test>\n+         <param name=\"file\" value=\"counts_no_header.tab\" ftype=\"tabular\"/>\n+         <param name=\"file_sep\" value=\"tab\"/>\n+         <param name=\"file_header\" value=\"FALSE\"/>\n+         <param name=\"is_mito\" value=\"FALSE\"/>\n+         <param name=\"package\" value=\"scater\"/>\n+         <param name=\"gene_filter\" value=\"low.abundances\"/>\n+         <param name=\"min_cells\" value=\"1\"/>\n+         <output name=\"output_plot\" file=\"counts_no_header_scater_low.abundances_filter_plots.pdf\" ftype=\"pdf\"/>\n+         <output name=\"output_matrix\" file=\"counts_no_header_scater_low.abundances_filtered.tab\" ftype=\"tabular\"/>\n+      </test>\n+      <test>\n+         <param name=\"file\" value=\"counts.tab\" ftype=\"tabular\"/>\n+         <param name=\"file_sep\" value=\"tab\"/>\n+         <param name=\"file_header\" value=\"TRUE\"/>\n+         <param name=\"is_mito\" value=\"FALSE\"/>\n+         <param name=\"package\" value=\"scater\"/>\n+         <param name=\"gene_filter\" value=\"low.abundances\"/>\n+         <param name=\"min_cells\" value=\"1\"/>\n+         <output name=\"output_plot\" file=\"counts_scater_low.abundances_filter_plots.pdf\" ftype=\"pdf\"/>\n+         <output name=\"output_matrix\" file=\"counts_scater_low.abundances_filtered.tab\" ftype=\"tabular\"/>\n+      </test>\n+      <test>\n+         <param name=\"file\" value=\"counts.tab\" ftype=\"tabular\"/>\n+         <param name=\"file_sep\" value=\"tab\"/>\n+         <param name=\"file_header\" value=\"TRUE\"/>\n+         <param name=\"is_mito\" value=\"FALSE\"/>\n+         <param name=\"package\" value=\"scater\"/>\n+         <param name=\"gene_filter\" value=\"min.cells\"/>\n+         <param name=\"min_cells\" value=\"3\"/>\n+         <output name=\"output_plot\" file=\"counts_scater_min.cells_filter_plots.pdf\" ftype=\"pdf\"/>\n+         <output name=\"output_matrix\" file=\"counts_scater_min.cells_filtered.tab\" ftype=\"tabular\"/>\n+    </test>\n+\n+    <test>\n+         <param name=\"file\" value=\"counts.tab\" ftype=\"tabular\"/>\n+         <param name=\"file_sep\" value=\"tab\"/>\n+         <param name=\"file_header\" value=\"TRUE\"/>\n+         <param name=\"is_mito\" value=\"FALSE\"/>\n+         <param name=\"package\" value=\"Seurat\"/>\n+         <param name=\"min_genes\" value=\"10\"/>\n+         <param name=\"min_cells\" value=\"3\"/>\n+         <output name=\"output_plot\" file=\"counts_Seurat_filter_plots.pdf\" ftype=\"pdf\"/>\n+         <output name=\"output_matrix\" file=\"counts_Seurat_filtered.tab\" ftype=\"tabular\"/>\n+    </test>\n+    <test>\n+         <param name=\"file\" value=\"counts_with_mito.tab\" ftype=\"tabular\"/>\n+         <param name=\"file_sep\" value=\"tab\"/>\n+         <param name=\"file_header\" value=\"TRUE\"/>\n+         <param name=\"is_mito\" value=\"TRUE\"/>\n+         <param name=\"header_mito\" value=\"MT-\"/>\n+         <param name=\"package\" value=\"scater\"/>\n+         <param name=\"gene_filter\" value=\"low.abundances\"/>\n+         <param name=\"min_cells\" value=\"1\"/>\n+         <output name=\"output_plot\" file=\"counts_with_mito_scater_low.abundances_filter_plots.pdf\" ftype=\"pdf\"/>\n+         <output name=\"output_matrix\" file=\"counts_with_mito_scater_low.abundances_filtered.tab\" ftype=\"tabular\"/>\n+    </test>\n+    <test>\n+         <param name=\"file\" value=\"counts_with_mito.tab\" ftype=\"tabular\"/>\n+         <param name=\"file_sep\" value=\"tab\"/>\n+         <param name=\"file_header\" value=\"TRUE\"/>\n+         <param name=\"is_mito\" value=\"TRUE\"/>\n+         <param name=\"header_mito\" value=\"MT-\"/>\n+         <param name=\"package\" value=\"scater\"/>\n+         <param name=\"gene_filter\" value=\"min.cells\"/>\n+         <param name=\"min_cells\" value=\"3\"/>\n+         <output name=\"output_plot\" file=\"counts_with_mito_scater_min.cells_filter_plots.pdf\" ftype=\"pdf\"/>\n+         <output name=\"output_matrix\" file=\"counts_with_mito_scater_min.cells_filtered.tab\" ftype=\"tabular\"/>\n+    </test>\n+    <test>\n+         <param name=\"file\" value=\"counts_with_mito.tab\" ftype=\"tabular\"/>\n+         <param name=\"file_sep\" value=\"tab\"/>\n+         <param name=\"file_header\" value=\"TRUE\"/>\n+         <param name=\"is_mito\" value=\"TRUE\"/>\n+         <param name=\"header_mito\" value=\"MT-\"/>\n+         <param name=\"package\" value=\"Seurat\"/>\n+         <param name=\"min_genes\" value=\"10\"/>\n+         <param name=\"min_cells\" value=\"3\"/>\n+         <output name=\"output_plot\" file=\"counts_with_mito_Seurat_filter_plots.pdf\" ftype=\"pdf\"/>\n+         <output name=\"output_matrix\" file=\"counts_with_mito_Seurat_filtered.tab\" ftype=\"tabular\"/>\n+    </test> \n+   </tests>\n+   <help>\n+\n+**What it does**\n+\n+Filter_cells_and_genes takes a tabular table of raw read counts, each column corresponding to a cell and each row corresponding to a\n+gene, and returns (1) a PDF with quality controls plots (like the distribution of library sizes or expressed genes by cell, frequency of \n+expression or the most expressed genes) and (2) a filtered table of counts.\n+\n+You can filter out low quality cells from your raw expression table :\n+\n+- Based on expression level of mitochondrial genes :\n+\n+    - Using R package scater: remove cells that detect mitochondrial genes 3 times higher than the median of all cells\n+    - Using R package Seurat: if cells expressed more than 20% of mitochondrial genes, they are removed.\n+\n+- Using R package scater : search cells with low library size and few detected genes based on the deviation from the median of all cel$\n+\n+- Using R package Seurat : Remove all cells that detected at least n genes.\n+\n+Also you can filter out low quality genes from your raw expression table :\n+\n+- Using R package scater :\n+\n+    - Remove all genes that aren't detected in at least n cells\n+    - Filter out genes based on its average count (which is adjust for library size between cells). It is more stringent.\n+\n+- Using R package Seurat : Remove all genes that aren't detected in at least n cells.\n+\n+\n+**Inputs**\n+\n+The following table gives an example of the tabular input that has to be provided to the tool:\n+\n+\n+<![CDATA[\n+\n+AGTCAGACTAGAGAAGTCCAGATTTCAC\tAGTCTACTTGCATG\tAGTGTTCTATAAGG\tAGTGTTCTCACTTT\tAGTTCTTGAAGCCT\tATAAACACAGTGCT\tATAACCCTGTTGGT\tATAATCGAGCTGAT\tATACCACTCGTACA  \n+\n+MALAT1\t34\t78\t45\t86\t12\t46\t72\t76\t33\t19  \n+\n+TMSB4X\t32\t33\t109\t27\t46\t25\t31\t43\t11\t46  \n+\n+B2M\t53\t64\t93\t21\t10\t40\t33\t33\t18\t15  \n+\n+RPL10\t35\t19\t36\t24\t35\t20\t16\t24\t32\t32  \n+\n+RPL13\t26\t23\t37\t17\t28\t12\t32\t24\t18\t56  \n+\n+RPL13A\t16\t32\t38\t24\t21\t10\t18\t30\t19\t25  \n+\n+FTL\t2\t4\t175\t6\t101\t6\t31\t2\t1\t54  \n+\n+RPS2\t17\t20\t32\t8\t35\t10\t23\t20\t12\t24  \n+\n+RPS6\t57\t20\t28\t15\t25\t14\t24\t29\t13\t17  \n+\n+FTH1\t6\t7\t151\t2\t22\t5\t9\t7\t4\t45  \n+\n+RPS18\t9\t25\t19\t16\t17\t8\t21\t26\t9\t19  \n+\n+RPL11\t19\t15\t30\t14\t21\t7\t13\t15\t8\t64  \n+\n+RPL32\t14\t16\t30\t15\t30\t10\t15\t17\t13\t22  \n+\n+RPS3\t9\t19\t12\t12\t12\t11\t16\t18\t4\t11  \n+\n+RPL19\t16\t16\t27\t10\t70\t11\t16\t14\t11\t17  \n+\n+MT-ND1\t2\t0\t5\t1\t6\t4\t6\t3\t2\t5  \n+\n+MT-ND2\t4\t4\t15\t2\t0\t1\t3\t9\t0\t8  \n+\n+MT-CO1\t11\t3\t52\t10\t9\t14\t11\t9\t9\t22  \n+\n+MT-CO2\t4\t5\t35\t8\t5\t2\t7\t10\t2\t7  \n+\n+MT-ATP8\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0  \n+\n+","path":"tools/filter_cells_and_genes/filter_cells_and_genes.xml","position":255,"original_position":255,"commit_id":"52aa60d3333890e3d334a3ef40a172bd5a8d5e01","original_commit_id":"52aa60d3333890e3d334a3ef40a172bd5a8d5e01","user":{"login":"drosofff","id":11705625,"node_id":"MDQ6VXNlcjExNzA1NjI1","avatar_url":"https://avatars3.githubusercontent.com/u/11705625?v=4","gravatar_id":"","url":"https://api.github.com/users/drosofff","html_url":"https://github.com/drosofff","followers_url":"https://api.github.com/users/drosofff/followers","following_url":"https://api.github.com/users/drosofff/following{/other_user}","gists_url":"https://api.github.com/users/drosofff/gists{/gist_id}","starred_url":"https://api.github.com/users/drosofff/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/drosofff/subscriptions","organizations_url":"https://api.github.com/users/drosofff/orgs","repos_url":"https://api.github.com/users/drosofff/repos","events_url":"https://api.github.com/users/drosofff/events{/privacy}","received_events_url":"https://api.github.com/users/drosofff/received_events","type":"User","site_admin":false},"body":"** Outputs **\r\n\r\nAnd here we are. Sorry Lea but you will  have to explain every possible output, especially the pdf. This is the (nice) job: explaining the outputs is just *Science* - and make all difference with bad \"have to guess\" tools !","created_at":"2018-11-15T18:13:22Z","updated_at":"2018-11-15T18:16:15Z","html_url":"https://github.com/ARTbio/tools-artbio/pull/317#discussion_r233953528","pull_request_url":"https://api.github.com/repos/ARTbio/tools-artbio/pulls/317","author_association":"MEMBER","_links":{"self":{"href":"https://api.github.com/repos/ARTbio/tools-artbio/pulls/comments/233953528"},"html":{"href":"https://github.com/ARTbio/tools-artbio/pull/317#discussion_r233953528"},"pull_request":{"href":"https://api.github.com/repos/ARTbio/tools-artbio/pulls/317"}}},"pull_request":{"url":"https://api.github.com/repos/ARTbio/tools-artbio/pulls/317","id":226153206,"node_id":"MDExOlB1bGxSZXF1ZXN0MjI2MTUzMjA2","html_url":"https://github.com/ARTbio/tools-artbio/pull/317","diff_url":"https://github.com/ARTbio/tools-artbio/pull/317.diff","patch_url":"https://github.com/ARTbio/tools-artbio/pull/317.patch","issue_url":"https://api.github.com/repos/ARTbio/tools-artbio/issues/317","number":317,"state":"open","locked":false,"title":"Add tool : Filter_cells_and_genes","user":{"login":"bellenger-l","id":32295405,"node_id":"MDQ6VXNlcjMyMjk1NDA1","avatar_url":"https://avatars0.githubusercontent.com/u/32295405?v=4","gravatar_id":"","url":"https://api.github.com/users/bellenger-l","html_url":"https://github.com/bellenger-l","followers_url":"https://api.github.com/users/bellenger-l/followers","following_url":"https://api.github.com/users/bellenger-l/following{/other_user}","gists_url":"https://api.github.com/users/bellenger-l/gists{/gist_id}","starred_url":"https://api.github.com/users/bellenger-l/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bellenger-l/subscriptions","organizations_url":"https://api.github.com/users/bellenger-l/orgs","repos_url":"https://api.github.com/users/bellenger-l/repos","events_url":"https://api.github.com/users/bellenger-l/events{/privacy}","received_events_url":"https://api.github.com/users/bellenger-l/received_events","type":"User","site_admin":false},"body":"Add new tool that can filter cells(columns) and genes (row) from an expression matrix based on different quality controls.\r\n","created_at":"2018-10-26T16:18:07Z","updated_at":"2018-11-15T18:16:15Z","closed_at":null,"merged_at":null,"merge_commit_sha":"a17928b0a83acee815657e0e9d627158e8a2c84c","assignee":null,"assignees":[],"requested_reviewers":[],"requested_teams":[],"labels":[],"milestone":null,"commits_url":"https://api.github.com/repos/ARTbio/tools-artbio/pulls/317/commits","review_comments_url":"https://api.github.com/repos/ARTbio/tools-artbio/pulls/317/comments","review_comment_url":"https://api.github.com/repos/ARTbio/tools-artbio/pulls/comments{/number}","comments_url":"https://api.github.com/repos/ARTbio/tools-artbio/issues/317/comments","statuses_url":"https://api.github.com/repos/ARTbio/tools-artbio/statuses/52aa60d3333890e3d334a3ef40a172bd5a8d5e01","head":{"label":"ARTbio:celebration_filter","ref":"celebration_filter","sha":"52aa60d3333890e3d334a3ef40a172bd5a8d5e01","user":{"login":"ARTbio","id":13965324,"node_id":"MDEyOk9yZ2FuaXphdGlvbjEzOTY1MzI0","avatar_url":"https://avatars0.githubusercontent.com/u/13965324?v=4","gravatar_id":"","url":"https://api.github.com/users/ARTbio","html_url":"https://github.com/ARTbio","followers_url":"https://api.github.com/users/ARTbio/followers","following_url":"https://api.github.com/users/ARTbio/following{/other_user}","gists_url":"https://api.github.com/users/ARTbio/gists{/gist_id}","starred_url":"https://api.github.com/users/ARTbio/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ARTbio/subscriptions","organizations_url":"https://api.github.com/users/ARTbio/orgs","repos_url":"https://api.github.com/users/ARTbio/repos","events_url":"https://api.github.com/users/ARTbio/events{/privacy}","received_events_url":"https://api.github.com/users/ARTbio/received_events","type":"Organization","site_admin":false},"repo":{"id":41668246,"node_id":"MDEwOlJlcG9zaXRvcnk0MTY2ODI0Ng==","name":"tools-artbio","full_name":"ARTbio/tools-artbio","private":false,"owner":{"login":"ARTbio","id":13965324,"node_id":"MDEyOk9yZ2FuaXphdGlvbjEzOTY1MzI0","avatar_url":"https://avatars0.githubusercontent.com/u/13965324?v=4","gravatar_id":"","url":"https://api.github.com/users/ARTbio","html_url":"https://github.com/ARTbio","followers_url":"https://api.github.com/users/ARTbio/followers","following_url":"https://api.github.com/users/ARTbio/following{/other_user}","gists_url":"https://api.github.com/users/ARTbio/gists{/gist_id}","starred_url":"https://api.github.com/users/ARTbio/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ARTbio/subscriptions","organizations_url":"https://api.github.com/users/ARTbio/orgs","repos_url":"https://api.github.com/users/ARTbio/repos","events_url":"https://api.github.com/users/ARTbio/events{/privacy}","received_events_url":"https://api.github.com/users/ARTbio/received_events","type":"Organization","site_admin":false},"html_url":"https://github.com/ARTbio/tools-artbio","description":"Collection 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