Mercurial > repos > iuc > genrich
comparison genrich.xml @ 1:db50f51a2952 draft
"planemo upload for repository https://github.com/jsh58/Genrich commit 85e0bb6eaeaf1b82357cb95abf6ebad6dd4ab492"
| author | iuc |
|---|---|
| date | Sat, 17 Aug 2019 16:24:04 -0400 |
| parents | a41d96fc0b20 |
| children | 8353f3cc03db |
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| 0:a41d96fc0b20 | 1:db50f51a2952 |
|---|---|
| 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> |