Mercurial > repos > pjbriggs > weeder2
comparison weeder2_wrapper.xml @ 2:3c5f10f7dd40 draft
Updated to tool version 2.0.1 (use data table to locate freqfiles).
author | pjbriggs |
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date | Fri, 27 Nov 2015 11:06:28 -0500 |
parents | 571cb77ab9e7 |
children | f19e18ab01b1 |
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1:571cb77ab9e7 | 2:3c5f10f7dd40 |
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1 <tool id="motiffinding_weeder2" name="Weeder2" version="2.0.0"> | 1 <tool id="motiffinding_weeder2" name="Weeder2" version="2.0.1"> |
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 <requirements> | |
4 <requirement type="package" version="2.0">weeder</requirement> | |
5 </requirements> | |
3 <command interpreter="bash">weeder2_wrapper.sh | 6 <command interpreter="bash">weeder2_wrapper.sh |
4 $sequence_file $species_code | 7 $sequence_file $species_code ${species_code.fields.path} |
5 $output_motifs_file $output_matrix_file | 8 $output_motifs_file $output_matrix_file |
6 $strands | 9 $strands |
7 #if $chipseq.use_chipseq | 10 #if $chipseq.use_chipseq |
8 -chipseq -top $chipseq.top | 11 -chipseq -top $chipseq.top |
9 #end if | 12 #end if |
11 -maxm $advanced_options.n_motifs_report | 14 -maxm $advanced_options.n_motifs_report |
12 -b $advanced_options.n_motifs_build | 15 -b $advanced_options.n_motifs_build |
13 -sim $advanced_options.sim_threshold | 16 -sim $advanced_options.sim_threshold |
14 -em $advanced_options.em_cycles | 17 -em $advanced_options.em_cycles |
15 #end if | 18 #end if |
16 </command> | 19 </command> |
17 <requirements> | |
18 <requirement type="package" version="2.0">weeder</requirement> | |
19 </requirements> | |
20 <inputs> | 20 <inputs> |
21 <param name="sequence_file" type="data" format="fasta" label="Input sequence" /> | 21 <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"> | 22 <param name="species_code" type="select" label="Species to use for background comparison"> |
23 <!-- Hard code options for now | 23 <options from_data_table="weeder2"> |
24 See weeder's "organisms.txt" for full list | 24 </options> |
25 --> | |
26 <option value="HS">Homo sapiens (HS)</option> | |
27 <option value="MM">Mus musculus (MM)</option> | |
28 <option value="DM">Drosophila melanogaster (DM)</option> | |
29 <option value="SC">Saccharomyces cerevisiae (SC)</option> | |
30 <option value="AT">Arabidopsis thaliana (AT)</option> | |
31 </param> | 25 </param> |
32 <param name="strands" label="Use both strands of sequence" type="boolean" | 26 <param name="strands" label="Use both strands of sequence" type="boolean" |
33 truevalue="" falsevalue="-ss" checked="True" | 27 truevalue="" falsevalue="-ss" checked="True" |
34 help="If not checked then use -ss option" /> | 28 help="If not checked then use -ss option" /> |
35 <conditional name="chipseq"> | 29 <conditional name="chipseq"> |