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comparison genrich.xml @ 1:65ea5e60e6b0 draft

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"planemo upload for repository https://github.com/jsh58/Genrich commit 85e0bb6eaeaf1b82357cb95abf6ebad6dd4ab492"
author iuc
date Sat, 17 Aug 2019 16:23:09 -0400
parents 48c5ff6b11fb
children bb2fb6a25c21
comparison
equal deleted inserted replaced
0:48c5ff6b11fb 1:65ea5e60e6b0
1 <tool id="genrich" name="Genrich" version="0.5"> 1 <tool id="genrich" name="Genrich" version="0.5+galaxy1">
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>
36 #################### 36 ####################
37 ## Filter Options ## 37 ## Filter Options ##
38 #################### 38 ####################
39 39
40 #if $filter_options.duplicates: 40 #if $filter_options.duplicates:
41 '$filter_options.duplicates' '${out_dups}' 41 -r -R '${out_dups}'
42 #end if 42 #end if
43 43
44 #if $filter_options.exclude_chr: 44 #if $filter_options.exclude_chr:
45 -e '$filter_options.exclude_chr' 45 -e '$filter_options.exclude_chr'
46 #end if 46 #end if
116 <param name="t_multi_select" type="select" label="Are you pooling Treatment Files?" help="For more information, see Help section below" > 116 <param name="t_multi_select" type="select" label="Are you pooling Treatment Files?" help="For more information, see Help section below" >
117 <option value="No" selected="True">No</option> 117 <option value="No" selected="True">No</option>
118 <option value="Yes">Yes</option> 118 <option value="Yes">Yes</option>
119 </param> 119 </param>
120 <when value="No" > 120 <when value="No" >
121 <param name="input_treatment_file" argument="-t" type="data" format="qname_sorted.bam" label="Treatment File(s)" /> 121 <param name="input_treatment_file" argument="-t" type="data" format="qname_sorted.bam" label="Treatment File"
122 help="This file should be a name-sorted BAM file. 'samtools sort' can do this with the 'name (-n)' parameter." />
122 </when> 123 </when>
123 <when value="Yes"> 124 <when value="Yes">
124 <param name="input_treatment_file" argument="-t" type="data" format="qname_sorted.bam" multiple="true" label="Treatment Files" /> 125 <param name="input_treatment_file" argument="-t" type="data" format="qname_sorted.bam" multiple="true"
126 label="Treatment Files."
127 help="These files should be a name-sorted BAM file. 'samtools sort' can do this with the 'name (-n)' parameter." />
125 </when> 128 </when>
126 </conditional> 129 </conditional>
127 130
128 <conditional name="control"> 131 <conditional name="control">
129 <param name="c_select" type="select" label="Do you have a Control File?" > 132 <param name="c_select" type="select" label="Do you have a Control File?" >
135 <param name="c_multi_select" type="select" label="Are you pooling Control Files?" help="For more information, see Help section below" > 138 <param name="c_multi_select" type="select" label="Are you pooling Control Files?" help="For more information, see Help section below" >
136 <option value="No" selected="True">No</option> 139 <option value="No" selected="True">No</option>
137 <option value="Yes">Yes</option> 140 <option value="Yes">Yes</option>
138 </param> 141 </param>
139 <when value="No" > 142 <when value="No" >
140 <param name="input_control_file" argument="-c" type="data" format="qname_sorted.bam" label="Control File(s)" /> 143 <param name="input_control_file" argument="-c" type="data" format="qname_sorted.bam" label="Control File"
144 help="This file should be a name-sorted BAM file. 'samtools sort' can do this with the 'name (-n)' parameter." />
141 </when> 145 </when>
142 <when value="Yes"> 146 <when value="Yes">
143 <param name="input_control_file" argument="-c" type="data" format="qname_sorted.bam" multiple="true" label="Control Files" /> 147 <param name="input_control_file" argument="-c" type="data" format="qname_sorted.bam" multiple="true" label="Control Files"
148 help="These files should be a name-sorted BAM file. 'samtools sort' can do this with the 'name (-n)' parameter." />
144 </when> 149 </when>
145 </conditional> 150 </conditional>
146 </when> 151 </when>
147 <when value="No" /> 152 <when value="No" />
148 </conditional> 153 </conditional>