Mercurial > repos > kevyin > homer
comparison makeTagDirectory.xml @ 2:7268cbc535e5 draft
findpeaks and maketagdirectory
author | kevyin |
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date | Fri, 23 Nov 2012 00:30:27 -0500 |
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1:59d58008c40d | 2:7268cbc535e5 |
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1 <tool id="homer_makeTagDirectory" name="homer_makeTagDirectory" version="0.0.8"> | |
2 <requirements> | |
3 <requirement type="package" >homer</requirement> | |
4 </requirements> | |
5 <description>makeTagDirectory</description> | |
6 <version_command>echo "Doh!"</version_command> | |
7 <command> makeTagDirectory ${tagDir.extra_files_path} | |
8 #for $alignF in $alignmentFiles | |
9 $alignF.file -format $alignF.file.ext | |
10 #end for | |
11 2> $out_log || echo "Error running homer_makeTagDirectory." >&2 | |
12 | |
13 </command> | |
14 <inputs> | |
15 <param name="title" label="Name for the output tag directory" type="text" default="Homer TagDirectory" /> | |
16 <repeat name="alignmentFiles" title="Alignment Files"> | |
17 <param name="file" label="Add file" type="data" format="sam,bed" /> | |
18 </repeat> | |
19 </inputs> | |
20 <outputs> | |
21 <data format="homerTagDirectory" name="tagDir" label="${title}" /> | |
22 <data format="txt" name="out_log" label="${title}.log" /> | |
23 <!--<data format="html" name="html_outfile" label="index" />--> | |
24 <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />--> | |
25 </outputs> | |
26 | |
27 | |
28 <tests> | |
29 <!--<test>--> | |
30 <!--<param name="input_file" value="extract_genomic_dna.fa" />--> | |
31 <!--<output name="html_file" file="sample_output.html" ftype="html" />--> | |
32 <!--</test>--> | |
33 </tests> | |
34 | |
35 <help> | |
36 | |
37 .. class:: infomark | |
38 | |
39 After the job finishes, save the zip file, unzip and open "index.html" | |
40 | |
41 The actual meme-chip command is displayed under "Command line summary" | |
42 | |
43 Defaults: | |
44 http://meme.nbcr.net/meme/doc/meme-chip.html | |
45 | |
46 </help> | |
47 </tool> | |
48 |