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comparison genrich.xml @ 2:8353f3cc03db draft default tip

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"planemo upload for repository https://github.com/jsh58/Genrich commit 62a6ec655d7743ce084e45ba02b495e8bd2dc06c"
author iuc
date Thu, 29 Aug 2019 10:42:38 -0400
parents db50f51a2952
children
comparison
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1:db50f51a2952 2:8353f3cc03db
1 <tool id="genrich" name="Genrich" version="0.5+galaxy1"> 1 <tool id="genrich" name="Genrich" version="0.5+galaxy2">
2 <description>Detecting sites of genomic enrichment</description> 2 <description>Detecting sites of genomic enrichment</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.5">genrich</requirement> 4 <requirement type="package" version="0.5">genrich</requirement>
5 <requirement type="package" version="1.9">samtools</requirement> 5 <requirement type="package" version="1.9">samtools</requirement>
6 </requirements> 6 </requirements>
17 ## Input ## 17 ## Input ##
18 ########### 18 ###########
19 19
20 ## Treatment File(s) 20 ## Treatment File(s)
21 #if str($treatment.t_multi_select) == "Yes": 21 #if str($treatment.t_multi_select) == "Yes":
22 -t ${ ' '.join( [ "'%s'" % $x for $x in $treatment.input_treatment_file] ) } 22 -t ${ ','.join( [ "'%s'" % $x for $x in $treatment.input_treatment_file] ) }
23 #else 23 #else
24 -t '$treatment.input_treatment_file' 24 -t '$treatment.input_treatment_file'
25 #end if 25 #end if
26 26
27 ## Control File(s) 27 ## Control File(s)
28 #if str($control.c_select) == "Yes": 28 #if str($control.c_select) == "Yes":
29 #if str($control.c_multiple.c_multi_select) == "Yes": 29 #if str($control.c_multiple.c_multi_select) == "Yes":
30 -c ${ ' '.join( [ "'%s'" % $x for $x in $control.c_multiple.input_control_file] ) } 30 -c ${ ','.join( [ "'%s'" % $x for $x in $control.c_multiple.input_control_file] ) }
31 #else 31 #else
32 -c '$control.c_multiple.input_control_file' 32 -c '$control.c_multiple.input_control_file'
33 #end if 33 #end if
34 #end if 34 #end if
35 35
249 <output name="outfile" ftype="encodepeak" file="CTCF.encodepeak" /> 249 <output name="outfile" ftype="encodepeak" file="CTCF.encodepeak" />
250 <output name="out_bedgraph1" ftype="bedgraph" file="CTCF1.bedgraph" /> 250 <output name="out_bedgraph1" ftype="bedgraph" file="CTCF1.bedgraph" />
251 <output name="out_bedgraph2" ftype="bedgraph" file="CTCF2.bedgraph" compare="contains" lines_diff="1" /> 251 <output name="out_bedgraph2" ftype="bedgraph" file="CTCF2.bedgraph" compare="contains" lines_diff="1" />
252 <output name="out_bed" ftype="bed" file="CTCF.bed" /> 252 <output name="out_bed" ftype="bed" file="CTCF.bed" />
253 </test> 253 </test>
254 <!-- ChIP Test Data for Pooled Data (Replicates)-->
255 <test expect_num_outputs="4">
256 <param name="input_treatment_file" ftype="bam" value="CTCF_PE_ChIP_chr22.bam,CTCF_PE_ChIP_chr22_2.bam" />
257 <param name="input_control_file" ftype="bam" value="CTCF_PE_CTRL_chr22.bam,CTCF_PE_CTRL_chr22_2.bam" />
258 <param name="c_select" value="Yes" />
259 <param name="t_multi_select" value="Yes" />
260 <param name="c_multi_select" value="Yes" />
261 <param name="bedgraph1" value="True" />
262 <param name="bedgraph2" value="True" />
263 <param name="bed" value="True" />
264 <output name="outfile" ftype="encodepeak" file="Pool.encodepeak" />
265 <output name="out_bedgraph1" ftype="bedgraph" file="Pool1.bedgraph" />
266 <output name="out_bedgraph2" ftype="bedgraph" file="Pool2.bedgraph" compare="contains" lines_diff="2" />
267 <output name="out_bed" ftype="bed" file="Pool.bed" />
268 </test>
254 </tests> 269 </tests>
255 <help><![CDATA[ 270 <help><![CDATA[
256 271
257 .. class:: infomark 272 .. class:: infomark
258 273