Mercurial > repos > pjbriggs > weeder2

comparison weeder2_wrapper.xml @ 3:f19e18ab01b1 draft

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Uploaded v2.0.2 (use conda for dependency resolution)
author pjbriggs
date Mon, 05 Mar 2018 10:19:50 -0500
parents 3c5f10f7dd40
children 89315bdc1a8c
comparison
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2:3c5f10f7dd40 3:f19e18ab01b1
1 <tool id="motiffinding_weeder2" name="Weeder2" version="2.0.1"> 1 <tool id="motiffinding_weeder2" name="Weeder2" version="2.0.2">
2 <description>Motif discovery in sequences from coregulated genes of a single species</description> 2 <description>Motif discovery in sequences from coregulated genes of a single species</description>
3 <macros>
4 <import>weeder2_macros.xml</import>
5 </macros>
3 <requirements> 6 <requirements>
4 <requirement type="package" version="2.0">weeder</requirement> 7 <requirement type="package" version="2.0">weeder</requirement>
5 </requirements> 8 </requirements>
6 <command interpreter="bash">weeder2_wrapper.sh 9 <command><![CDATA[
10 @CONDA_WEEDER2_FREQFILES_PATH@ &&
11 bash $__tool_directory__/weeder2_wrapper.sh
7 $sequence_file $species_code ${species_code.fields.path} 12 $sequence_file $species_code ${species_code.fields.path}
8 $output_motifs_file $output_matrix_file 13 $output_motifs_file $output_matrix_file
9 $strands 14 $strands
10 #if $chipseq.use_chipseq 15 #if $chipseq.use_chipseq
11 -chipseq -top $chipseq.top 16 -chipseq -top $chipseq.top
14 -maxm $advanced_options.n_motifs_report 19 -maxm $advanced_options.n_motifs_report
15 -b $advanced_options.n_motifs_build 20 -b $advanced_options.n_motifs_build
16 -sim $advanced_options.sim_threshold 21 -sim $advanced_options.sim_threshold
17 -em $advanced_options.em_cycles 22 -em $advanced_options.em_cycles
18 #end if 23 #end if
19 </command> 24 ]]></command>
20 <inputs> 25 <inputs>
21 <param name="sequence_file" type="data" format="fasta" label="Input sequence" /> 26 <param name="sequence_file" type="data" format="fasta" label="Input sequence" />
22 <param name="species_code" type="select" label="Species to use for background comparison"> 27 <param name="species_code" type="select" label="Species to use for background comparison">
23 <options from_data_table="weeder2"> 28 <options from_data_table="weeder2">
24 </options> 29 </options>