Mercurial > repos > da-intersect > ap11_test

annotate samifier.xml @ 5:795f289b64db draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
First complete upload, containing the datatype TAR.
author da-intersect
date Wed, 10 Apr 2013 02:41:02 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
1 <tool id="samifier" name="Samifier" version="1.0.0">
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
2 <description>Samifier vX.X</description>
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
3 <command interpreter="bash">
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
4 samifier.sh samifier.jar $chromosome_tar -g "$genome" -m "$mapping" -o "$output1" -r "$mascot"
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
5 #if $score_thresold
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
6 -s "$score_thresold"
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
7 #end if
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
8 #if $condition2.tool_option2 == "yes"
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
9 -l "$output2"
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
10 #end if
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
11 #if $condition3.tool_option3 == "yes"
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
12 -b "$output3"
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
13 #end if
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
14 </command>
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
15 <inputs>
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
16 <param name="chromosome_tar" type="data" format="tar" label="Select chromosome zip files" help="A zip file containing all the chromosome files" />
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
17 <param name="genome" type="data" format="gff" label="Select genome file" help="Genome file in gff format" />
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
18 <param name="mascot" type="data" format="txt" label="Select Mascot search result" help="Mascot search results file in txt format" />
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
19 <param name="mapping" type="data" format="txt" label="Select file mapping" help="File mapping protein identifier to ordered locus name" />
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
20 <param name="score_thresold" type="integer" label="Confidence Score thresold" help="Minimum confidence score for peptides to" optional="true"/>
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
21
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
22 <conditional name="condition2">
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
23 <param name="tool_option2" type="select" label="Write log file" help="Create an output containing the logs">
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
24 <option value="yes" selected="No">Yes</option>
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
25 <option value="no" selected="Yes">No</option>
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
26 </param>
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
27 </conditional>
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
28 <conditional name="condition3">
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
29 <param name="tool_option3" type="select" label="Write output in bed format" help="Output to write IGV regions of interest">
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
30 <option value="yes" selected="No">Yes</option>
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
31 <option value="no" selected="Yes">No</option>
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
32 </param>
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
33 </conditional>
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
34 </inputs>
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
35 <outputs>
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
36 <data format="sam" name="output1" />
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
37 <data format="txt" name="output2" label="Samifier log file">
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
38 <filter>condition2['tool_option2'] == "yes"</filter>
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
39 </data>
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
40 <data format="bed" name="output3" label="Samifier Bed">
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
41 <filter>condition3['tool_option3'] == "yes"</filter>
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
42 </data>
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
43 </outputs>
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
44 <help>
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
45 </help>
795f289b64db First complete upload, containing the datatype TAR.
da-intersect
parents:
diff changeset
46 </tool>