Mercurial > repos > marc-wilkins > samifier
diff samifier/samifier.xml @ 2:66ad014e6975 draft default tip
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author | marc-wilkins |
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date | Tue, 06 Aug 2013 20:43:24 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samifier/samifier.xml Tue Aug 06 20:43:24 2013 -0400 @@ -0,0 +1,46 @@ +<tool id="samifier" name="Samifier" version="1.0.9"> + <description>Samifier</description> + <command interpreter="bash"> + samifier.sh samifier.jar $chromosome_tar -g "$genome" -m "$mapping" -o "$output1" -r "$mascot" + #if $score_thresold + -s "$score_thresold" + #end if + #if $condition2.tool_option2 == "yes" + -l "$output2" + #end if + #if $condition3.tool_option3 == "yes" + -b "$output3" + #end if + </command> + <inputs> + <param name="chromosome_tar" type="data" format="tar" label="Select chromosome zip files" help="A zip file containing all the chromosome files" /> + <param name="genome" type="data" format="gff" label="Select genome file" help="Genome file in gff format" /> + <param name="mascot" type="data" format="txt" label="Select Mascot search result" help="Mascot search results file in txt format" /> + <param name="mapping" type="data" format="txt" label="Select file mapping" help="File mapping protein identifier to ordered locus name" /> + <param name="score_thresold" type="integer" label="Confidence Score thresold" help="Minimum confidence score for peptides to" optional="true"/> + + <conditional name="condition2"> + <param name="tool_option2" type="select" label="Write log file" help="Create an output containing the logs"> + <option value="yes" selected="No">Yes</option> + <option value="no" selected="Yes">No</option> + </param> + </conditional> + <conditional name="condition3"> + <param name="tool_option3" type="select" label="Write output in bed format" help="Output to write IGV regions of interest"> + <option value="yes" selected="No">Yes</option> + <option value="no" selected="Yes">No</option> + </param> + </conditional> + </inputs> + <outputs> + <data format="sam" name="output1" /> + <data format="txt" name="output2" label="Samifier log file"> + <filter>condition2['tool_option2'] == "yes"</filter> + </data> + <data format="bed" name="output3" label="Samifier Bed"> + <filter>condition3['tool_option3'] == "yes"</filter> + </data> + </outputs> + <help> + </help> +</tool>