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comparison macs2_predictd.xml @ 49:1b3f899ef044 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
author iuc
date Sat, 08 Apr 2017 08:28:38 -0400
parents 9033b59bf9c1
children 8f6b37d29df5
comparison
equal deleted inserted replaced
48:e04fc51ee5e1 49:1b3f899ef044
1 <tool id="macs2_predictd" name="MACS2 predictd" version="@VERSION_STRING@.0"> 1 <tool id="macs2_predictd" name="MACS2 predictd" version="@VERSION_STRING@.0">
2 <description>Predict 'd' or fragment size from alignment results</description> 2 <description>Predict 'd' or fragment size from alignment results</description>
3 <macros> 3 <macros>
4 <import>macs2_macros.xml</import> 4 <import>macs2_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"> 6 <expand macro="requirements"/>
7 <requirement type="package" version="3.1.2">R</requirement>
8 <requirement type="package" version="4.1.0">gnu_awk</requirement>
9 </expand>
10 <expand macro="stdio" /> 7 <expand macro="stdio" />
11 <expand macro="version_command" /> 8 <expand macro="version_command" />
12 <command> 9 <command>
10 <![CDATA[
13 macs2 predictd 11 macs2 predictd
14 -i ${ ' '.join( map( lambda x:'"%s"' % ( x ), $infiles ) ) }
15 @tag_size@
16 @effective_genome_size@
17 --bw "${ band_width }"
18 --mfold "${ mfoldlo }" "${ mfoldhi }"
19 12
20 ## remove the timepoint and strip the output 13 -i ${ ' '.join(["'%s'" % $x for $x in $infiles ]) }
21 2>&amp;1 | awk -F: '{print $4}' | awk '{$1=$1}1' 14 @tag_size@
15 @effective_genome_size@
16 --bw '${ band_width }'
17 @mfold_command@
22 18
23 &gt; "${ outfile }" 19 ## remove the timepoint and strip the output
20 2>&1 | awk -F: '{print $4}' | awk '{$1=$1}1'
24 21
25 &amp;&amp; 22 > '${ outfile }'
23
24 &&
26 25
27 Rscript predictd 26 Rscript predictd
27 ]]>
28 </command> 28 </command>
29 <inputs> 29 <inputs>
30 <param name="infiles" type="data" format="bam,sam,bed" multiple="True" label="ChIP-seq alignment file" help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command. (-i)" /> 30 <param name="infiles" type="data" format="bam,sam,bed" multiple="True"
31 label="ChIP-seq alignment file"
32 help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command. (-i)" />
31 <expand macro="conditional_effective_genome_size" /> 33 <expand macro="conditional_effective_genome_size" />
32 <expand macro="tag_size" /> 34 <expand macro="tag_size" />
33 <expand macro="band_width" /> 35 <expand macro="band_width" />
34 36 <expand macro="mfold_options" />
35 <param name="mfoldlo" type="integer" label="Fold-enrichment lower limit" value="5"
36 help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>
37 <param name="mfoldhi" type="integer" label="Fold-enrichment upper-limit" value="50"
38 help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>
39
40 </inputs> 37 </inputs>
41 38
42 <outputs> 39 <outputs>
43 <data name="outfile" format="txt" label="${tool.name} on ${on_string} - d value" /> 40 <data name="outfile" format="txt" label="${tool.name} on ${on_string} - d value" />
44 <data name="outfile_image" from_work_dir="predictd_model.pdf" format="pdf" label="${tool.name} on ${on_string} - X-correlation image" /> 41 <data name="outfile_image" from_work_dir="predictd_model.pdf" format="pdf" label="${tool.name} on ${on_string} - X-correlation image" />
46 <tests> 43 <tests>
47 <test> 44 <test>
48 <param name="infiles" value="Control_200K.bed,ChIP_200K.bed" ftype="bed" /> 45 <param name="infiles" value="Control_200K.bed,ChIP_200K.bed" ftype="bed" />
49 <param name="effective_genome_size_options_selector" value="user_defined" /> 46 <param name="effective_genome_size_options_selector" value="user_defined" />
50 <param name="gsize" value="3300000000" /> 47 <param name="gsize" value="3300000000" />
51 <param name="tsize" value="-1.0"/> 48 <param name="tsize" value=""/>
52 <param name="band_width" value="300"/> 49 <param name="band_width" value="300"/>
53 <param name="mfoldlo" value="5"/> 50 <param name="lower" value="5"/>
54 <param name="mfoldhi" value="50"/> 51 <param name="upper" value="50"/>
55 <output name="outfile" file="predictd_on_ChIP_200K_and_Control_200K.txt"/> 52 <output name="outfile" file="predictd_on_ChIP_200K_and_Control_200K.txt"/>
56 <output name="outfile_image" file="predictd_on_ChIP_200K_and_Control_200K.pdf" compare="sim_size"/> 53 <output name="outfile_image" file="predictd_on_ChIP_200K_and_Control_200K.pdf" compare="sim_size"/>
57 </test> 54 </test>
58 </tests> 55 </tests>
59 <help> 56 <help>
57 <![CDATA[
60 **What it does** 58 **What it does**
61 59
62 predictd from macs2 60 This is **predictd** utility from the MACS2_ Package. It predicts the *d* value or fragment size from alignment results.
63 61
64 62 .. _MACS2: https://github.com/taoliu/MACS
65 Note that pair-end data is not supposed to work with this command.
66
67 63
68 @citation@ 64 @citation@
65 ]]>
66
69 </help> 67 </help>
70 <expand macro="citations" /> 68 <expand macro="citations" />
71 </tool> 69 </tool>