|
12
|
1 <tool id="homer_makeTagDirectory" name="homer_makeTagDirectory" version="1.0.1">
|
|
|
2 <requirements>
|
|
|
3 <requirement type="package" version="4.1">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> $out_log || echo "Error running homer_makeTagDirectory." >&2
|
|
|
13
|
|
|
14 </command>
|
|
|
15 <inputs>
|
|
|
16 <param name="title" label="Name for the output tag directory" type="text" default="Homer TagDirectory" />
|
|
|
17 <param type="text" name="options" label="Extra options" value="" help="Go to link below for more options">
|
|
|
18 <sanitizer>
|
|
|
19 <valid initial="string.printable">
|
|
|
20 <remove value="'"/>
|
|
|
21 <remove value="/"/>
|
|
|
22 </valid>
|
|
|
23 <mapping initial="none">
|
|
|
24 <add source="'" target="__sq__"/>
|
|
|
25 </mapping>
|
|
|
26 </sanitizer>
|
|
|
27 </param>
|
|
|
28 <repeat name="alignmentFiles" title="Alignment Files">
|
|
|
29 <param name="file" label="Add file" type="data" format="sam,bed" />
|
|
|
30 </repeat>
|
|
|
31 </inputs>
|
|
|
32 <outputs>
|
|
|
33 <!--<data format="homerTagDirectory" name="tagDir" label="${title} tag directory" />-->
|
|
|
34 <data format="html" name="tagDir" label="${title} tag directory" />
|
|
|
35 <data format="txt" name="out_log" label="${title}.log" />
|
|
|
36 <!--<data format="html" name="html_outfile" label="index" />-->
|
|
|
37 <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
|
|
|
38 </outputs>
|
|
|
39
|
|
|
40
|
|
|
41 <tests>
|
|
|
42 <!--<test>-->
|
|
|
43 <!--<param name="input_file" value="extract_genomic_dna.fa" />-->
|
|
|
44 <!--<output name="html_file" file="sample_output.html" ftype="html" />-->
|
|
|
45 <!--</test>-->
|
|
|
46 </tests>
|
|
|
47
|
|
|
48 <help>
|
|
|
49
|
|
|
50 .. class:: infomark
|
|
|
51
|
|
|
52 **Homer makeTagDirectory**
|
|
|
53
|
|
|
54 For more options, look under: "Command line options"
|
|
|
55
|
|
|
56 http://biowhat.ucsd.edu/homer/ngs/tagDir.html
|
|
|
57
|
|
|
58
|
|
|
59 </help>
|
|
|
60 </tool>
|
|
|
61
|
