Mercurial > repos > stemcellcommons > scdetools
changeset 0:b1d730728d5f default tip
Initial commit.
| author | Ilya Sytchev <isytchev@hsph.harvard.edu> |
|---|---|
| date | Mon, 07 Oct 2013 18:54:25 -0400 |
| parents | |
| children | |
| files | scde_list_compare.xml scde_list_intersect.xml scde_list_match.xml |
| diffstat | 3 files changed, 239 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scde_list_compare.xml Mon Oct 07 18:54:25 2013 -0400 @@ -0,0 +1,90 @@ +<tool id="scde-list-compare" name="SCDE ListCompare" version="1.0" hidden="false"> +<description>compare multiple lists against one or more selected reference lists</description> +<version_string>scde --version</version_string> + +<command interpreter="perl"> + scde compare --source $source + + #for $i in $lists + --file ${i.filename} + --column ${i.column} + --organism ${i.organism} + --symbol ${i.symbol_type} + #end for + --output $format + + #if str($output_html) != "None" + > $output_html + #else + > $output_tab + #end if +</command> + +<inputs> + <param name="source" type="select" label="Compare your gene lists to"> + <option value="wikipathways">Wikipathways</option> + <option value="genesigdb">GeneSigDB</option> + <option value="msigdb">MSigDB</option> + <option value="scd">SCDE Repository - Public</option> + </param> + + <repeat name="lists" title="Add List" min="2" > + <param name="filename" type="data" format="txt" label="Dataset" help="Select a list for comparison from your History." /> + + <param name="column" type="select" label="Gene Column" help="Select the column number corresponding to the gene identifier"> + <option value="1">c1</option> + <option value="2">c2</option> + <option value="3">c3</option> + <option value="4">c4</option> + <option value="5">c5</option> + <option value="6">c6</option> + <option value="7">c7</option> + <option value="8">c8</option> + <option value="9">c9</option> + <option value="10">c10</option> + </param> + + <param name="organism" type="select" label="Query Organism" help="Which organism do your gene lists come from?"> + <option value="human">Human</option> + <option value="mouse">Mouse</option> + </param> + + <param name="symbol_type" type="select" label="Query Gene ID Type" help="Select the gene identifier type to search with."> + <option value="symbol">Gene Symbol</option> + <option value="ensembl">Ensembl ID</option> + <option value="entrez">Entrez ID</option> + </param> + </repeat> + + <param name="format" type="select" label="Output Format" help="Select the Format for the Output File"> + <option value="html">HTML</option> + <option value="tab">Tab Delimited</option> + </param> +</inputs> + +<outputs> + <data format="html" name="output_html"> + <filter>format == "html"</filter> + </data> + <data format="tabular" name="output_tab"> + <filter>format == "tab"</filter> + </data> +</outputs> + +<help> +**What it does** + +This tool compares two or more sets of gene lists against one or more selected reference lists. + +----- + +.. class:: infomark + +Upload data in tabular format to your history using the "Get Data" -> "Upload File" tool. + +.. class:: infomark + +Additional lists may be added using the "Add new List" button. +</help> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scde_list_intersect.xml Mon Oct 07 18:54:25 2013 -0400 @@ -0,0 +1,42 @@ +<tool id="scde-intersect" name="SCDE Intersect" version="1.0" hidden="false"> + +<description>find common genes within multiple lists</description> + +<version_string>scde --version</version_string> + +<command interpreter="perl"> + scde intersect --output tab + #for $i in $lists + --file ${i.filename} --column ${i.column} + #end for + > $output +</command> + +<inputs> + <repeat name="lists" title="List"> + <param name="filename" type="data" format="tabular" label="Dataset" help="Select a list for comparison from your History" /> + <param name="column" type="data_column" data_ref="filename" label="Gene Column" help="Select the column number corresponding to the gene identifier" /> + </repeat> +</inputs> + +<outputs> + <data format="txt" name="output" /> +</outputs> + +<help> +**What it does** + +This tool compares one or more lists and displays the common elements found in the selected column. + +----- + +.. class:: infomark + +Upload data in tabular format to your history using the "Get Data" -> "Upload File" tool. + +.. class:: infomark + +Additional lists may be added using the "Add new List" button. +</help> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scde_list_match.xml Mon Oct 07 18:54:25 2013 -0400 @@ -0,0 +1,107 @@ +<?xml version="1.0"?> +<tool id="scde-list-match" name="SCDE ListMatch" version="1.0" hidden="false"> +<description>match a list against one or more selected reference gene lists</description> +<version_string>scde --version</version_string> + +<command interpreter="perl"> + scde match --source $source + --organism $organism + + #if str($symbol_type) != "" + --symbol $symbol_type + #end if + + #if $query.type == "file" + --file $query.filename + --column $query.column + #else + $query.source + #end if + --min-matches $min_matches + --output $format + + #if str($output_html) != "None" + > $output_html + #else + > $output_tab + #end if +</command> + +<inputs> + <param name="source" type="select" label="Compare your gene list to"> + <option value="wikipathways">Wikipathways</option> + <option value="genesigdb">GeneSigDB</option> + <option value="msigdb">MSigDB</option> + <option value="scd">SCDE Repository - Public</option> + </param> + + <param name="organism" type="select" label="Query Organism" help="Which organism did your gene list come from?"> + <option value="human">Human</option> + <option value="mouse">Mouse</option> + </param> + + <param name="symbol_type" type="select" label="Query Gene ID Type" help="Select the gene identifier type to search with."> + <option value="symbol">Gene Symbol</option> + <option value="ensembl">Ensembl ID</option> + <option value="entrez">Entrez ID</option> + </param> + + <conditional name="query"> + <param name="type" type="select" label="Query source" help="You may select a file from your User History or enter a list of genes as text."> + <option value="file">History File</option> + <option value="text">Enter Text</option> + </param> + + <when value="file"> + <param name="filename" format="txt" type="data" label="Query History File" help="Select a file from your History"/> + <param name="column" type="data_column" data_ref="filename" label="Query File Column Number" help="Column numbers start at 1. Verify that the column number corresponds to the Gene ID Type you specified."/> + </when> + + <when value="text"> + <param name="source" type="text" area="true" size="5x60" label="Query using Text Entry" help="Paste a list of gene symbols here, separated by a space, tab, new line or a comma."/> + </when> + </conditional> + + <param name="min_matches" type="select" label="Minimum Number of Matches" help="Select the minimum number of genes that must be matched per reference gene list."> + <option value="1">1</option> + <option value="2">2</option> + <option value="3">3</option> + <option value="4">4</option> + <option value="5">5</option> + </param> + + <param name="format" type="select" label="Output Format" help="Select the format for the output file."> + <option value="html">HTML</option> + <option value="tab">Tab Delimited</option> + </param> +</inputs> + +<outputs> + <data format="html" name="output_html"> + <filter>format == "html"</filter> + </data> + <data format="tabular" name="output_tab"> + <filter>format == "tab"</filter> + </data> +</outputs> + +<help> +**What it does** + +This tool compares a list of genes as a query against one or more selected reference lists. + +----- + +.. class:: infomark + +Please upload your data as a tab-delimited text file. If the column number does not appear as a dropdown menu, make sure the file type is 'Tabular'. + +----- + +**Screencast!** + +Watch the SCDE ListMatch Screencast_ (right click to open this link in another window). + +.. _Screencast: http://discovery.hsci.harvard.edu/screencasts/galaxy.html +</help> +</tool>