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comparison makeTagDirectory.xml @ 4:74c1fc7bb164 draft

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display tag directories with html
author kevyin
date Tue, 27 Nov 2012 02:34:33 -0500
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3:4ea55669f00e 4:74c1fc7bb164
1 <tool id="homer_makeTagDirectory" name="homer_makeTagDirectory" version="1.0.0">
2 <requirements>
3 <requirement type="package" >homer</requirement>
4 </requirements>
5 <description>Simple wrapper for makeTagDirectory. Used by findPeaks</description>
6 <!--<version_command></version_command>-->
7 <command interpreter="python">makeTagDirectory.py ${tagDir.files_path}
8 #for $alignF in $alignmentFiles
9 $alignF.file -f $alignF.file.ext
10 #end for
11 -o $tagDir
12 2&gt; $out_log || echo "Error running homer_makeTagDirectory." >&amp;2
13
14 </command>
15 <inputs>
16 <param name="title" label="Name for the output tag directory" type="text" default="Homer TagDirectory" />
17 <repeat name="alignmentFiles" title="Alignment Files">
18 <param name="file" label="Add file" type="data" format="sam,bed" />
19 </repeat>
20 </inputs>
21 <outputs>
22 <!--<data format="homerTagDirectory" name="tagDir" label="${title} tag directory" />-->
23 <data format="html" name="tagDir" label="${title} tag directory" />
24 <data format="txt" name="out_log" label="${title}.log" />
25 <!--<data format="html" name="html_outfile" label="index" />-->
26 <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
27 </outputs>
28
29
30 <tests>
31 <!--<test>-->
32 <!--<param name="input_file" value="extract_genomic_dna.fa" />-->
33 <!--<output name="html_file" file="sample_output.html" ftype="html" />-->
34 <!--</test>-->
35 </tests>
36
37 <help>
38
39 .. class:: infomark
40
41 After the job finishes, save the zip file, unzip and open "index.html"
42
43 The actual meme-chip command is displayed under "Command line summary"
44
45 Defaults:
46 http://meme.nbcr.net/meme/doc/meme-chip.html
47
48 </help>
49 </tool>
50