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comparison fimo.xml @ 6:4df8e9f58a53 draft default tip

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author greg
date Wed, 06 Jul 2016 10:25:06 -0400
parents 1f221102ac4d
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5:e85346ab5054 6:4df8e9f58a53
1 <tool id="meme_fimo" name="FIMO" version="4.11.0.3"> 1 <tool id="meme_fimo" name="FIMO" version="4.11.1.0">
2 <description>- Scan a set of sequences for motifs.</description> 2 <description>- Scan a set of sequences for motifs.</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="6.9.3">imagemagick</requirement> 4 <requirement type="package" version="1.3.20">graphicsmagick</requirement>
5 <requirement type="package" version="4.11.0">meme</requirement> 5 <requirement type="package" version="4.11.1">meme</requirement>
6 </requirements> 6 </requirements>
7 <command> 7 <command>
8 <![CDATA[ 8 <![CDATA[
9 mkdir -p output && 9 mkdir -p output &&
10 python $__tool_directory__/fimo_wrapper.py 10 python $__tool_directory__/fimo_wrapper.py
115 <param name="parse_genomic_coord" label="Check each sequence header for UCSC style genomic coordinates" type="select"> 115 <param name="parse_genomic_coord" label="Check each sequence header for UCSC style genomic coordinates" type="select">
116 <option value="no" selected="true">No</option> 116 <option value="no" selected="true">No</option>
117 <option value="yes">Yes</option> 117 <option value="yes">Yes</option>
118 </param> 118 </param>
119 <when value="yes"> 119 <when value="yes">
120 <param name="remove_duplicate_coords" type="boolean" truevalue="yes" falsevalue="no" label="Remove duplicate entries in unique GFF coordinates?" help="Remove duplicate entries as defined by the unique GFF coordinates" /> 120 <param name="remove_duplicate_coords" type="select" label="Remove duplicate entries in unique GFF coordinates?" help="Remove duplicate entries as defined by the unique GFF coordinates">
121 <option value="no" selected="true">No</option>
122 <option value="yes">Yes</option>
123 </param>
121 </when> 124 </when>
122 <when value="no"/> 125 <when value="no"/>
123 </conditional> 126 </conditional>
124 <conditional name="psp_cond"> 127 <conditional name="psp_cond">
125 <param name="psp_selector" type="select" label="Use position-specific priors?"> 128 <param name="psp_selector" type="select" label="Use position-specific priors?">
176 </when> 179 </when>
177 </conditional> 180 </conditional>
178 </actions> 181 </actions>
179 </data> 182 </data>
180 <data format="tabular" name="gff_outfile" label="${tool.name} on ${on_string} (almost-gff)"> 183 <data format="tabular" name="gff_outfile" label="${tool.name} on ${on_string} (almost-gff)">
181 <filter>options_type['output_separate_motifs'] == 'no'</filter> 184 <filter>options_type['options_type_selector'] == 'basic' or (options_type['options_type_selector'] == 'advanced' and options_type['output_separate_motifs'] == 'no')</filter>
182 <actions> 185 <actions>
183 <conditional name="fasta_type.fasta_type_selector"> 186 <conditional name="fasta_type.fasta_type_selector">
184 <when value="cached"> 187 <when value="cached">
185 <action type="metadata" name="dbkey"> 188 <action type="metadata" name="dbkey">
186 <option type="from_data_table" name="all_fasta" column="1" offset="0"> 189 <option type="from_data_table" name="all_fasta" column="1" offset="0">
191 </conditional> 194 </conditional>
192 </actions> 195 </actions>
193 </data> 196 </data>
194 <collection name="motifs" type="list" label="Motifs: ${tool.name} on ${on_string}"> 197 <collection name="motifs" type="list" label="Motifs: ${tool.name} on ${on_string}">
195 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="output" ext="gff" visible="false" /> 198 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="output" ext="gff" visible="false" />
196 <filter>options_type['output_separate_motifs'] == 'yes'</filter> 199 <filter>options_type['options_type_selector'] == 'advanced' and options_type['output_separate_motifs'] == 'yes'</filter>
197 </collection> 200 </collection>
198 <data format="cisml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)"> 201 <data format="cisml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)">
199 <actions> 202 <actions>
200 <conditional name="fasta_type.fasta_type_selector"> 203 <conditional name="fasta_type.fasta_type_selector">
201 <when value="cached"> 204 <when value="cached">