Mercurial > repos > greg > gene_family_classifier

comparison gene_family_classifier.xml @ 12:b75510484c16 draft

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Uploaded
author greg
date Wed, 04 Jan 2017 13:52:09 -0500
parents b0a29067fc35
children cddbb2f13c28
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11:b0a29067fc35 12:b75510484c16
35 --coding_sequences "$options_type.create_orthogroup_cond.coding_sequences" 35 --coding_sequences "$options_type.create_orthogroup_cond.coding_sequences"
36 #end if 36 #end if
37 #end if 37 #end if
38 --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds" 38 --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
39 --num_threads \${GALAXY_SLOTS:-4} 39 --num_threads \${GALAXY_SLOTS:-4}
40 #if str($classifier) == 'hmmscan' or str($classifier) == 'both':
41 # Eliminate the hmmscan.log file
42 && rm $src_dir/*.log
43 #end if
40 #if create_ortho_sequences: 44 #if create_ortho_sequences:
41 echo "Sequences classified into pre-computed orthologous plant gene family clusters: `ls $src_dir | wc -l` files" > $output && 45 && echo "Sequences classified into pre-computed orthologous plant gene family clusters: `ls $src_dir | wc -l` files" > $output
42 mv $src_dir/* $dest_dir 46 && mv $src_dir/* $dest_dir
43 #end if 47 #end if
44 ]]> 48 ]]>
45 </command> 49 </command>
46 <inputs> 50 <inputs>
47 <param name="input" format="fasta" type="data" label="Amino acids (proteins) sequences fasta file"/> 51 <param name="input" format="fasta" type="data" label="Amino acids (proteins) sequences fasta file"/>
97 <outputs> 101 <outputs>
98 <data name="output" format="txt" label="Sequences classified into gene family clusters on ${on_string}"> 102 <data name="output" format="txt" label="Sequences classified into gene family clusters on ${on_string}">
99 <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes'</filter> 103 <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes'</filter>
100 </data> 104 </data>
101 <collection name="transcripts" type="list"> 105 <collection name="transcripts" type="list">
102 <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" /> 106 <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" />
103 </collection> 107 </collection>
104 </outputs> 108 </outputs>
105 <tests> 109 <tests>
106 <test> 110 <test>
107 <param name="input" value="" ftype="fasta" /> 111 <param name="input" value="" ftype="fasta" />