Mercurial > repos > greg > gene_family_classifier

comparison gene_family_classifier.xml @ 15:9d4ec1102803 draft

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Uploaded
author greg
date Wed, 04 Jan 2017 14:51:30 -0500
parents 595088cc480a
children 1cf39b1af248
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14:595088cc480a 15:9d4ec1102803
13 <command> 13 <command>
14 <![CDATA[ 14 <![CDATA[
15 #if str($options_type.options_type_selector) == 'advanced' and str($options_type.create_orthogroup_cond.create_orthogroup) == 'yes': 15 #if str($options_type.options_type_selector) == 'advanced' and str($options_type.create_orthogroup_cond.create_orthogroup) == 'yes':
16 #import os 16 #import os
17 #set create_ortho_sequences = True 17 #set create_ortho_sequences = True
18 #set src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta') 18 #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
19 #set dest_dir = $output.extra_files_path 19 #set dest_dir = $output.extra_files_path
20 mkdir -p $dest_dir && 20 mkdir -p $dest_dir &&
21 #else: 21 #else:
22 #set create_ortho_sequences = False 22 #set create_ortho_sequences = False
23 #end if 23 #end if
39 #end if 39 #end if
40 --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds" 40 --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
41 --num_threads \${GALAXY_SLOTS:-4} 41 --num_threads \${GALAXY_SLOTS:-4}
42 #if str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both': 42 #if str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both':
43 #if str($save_hmmscan_log_cond.save_hmmscan_log) == 'yes': 43 #if str($save_hmmscan_log_cond.save_hmmscan_log) == 'yes':
44 && mv $src_dir/hmmscan.log $hmmscan_log 44 && mv geneFamilyClassification_dir/hmmscan.log $hmmscan_log
45 #else: 45 #else:
46 && rm $src_dir/hmmscan.log 46 && rm geneFamilyClassification_dir/hmmscan.log
47 #end if 47 #end if
48 #end if 48 #end if
49 #if $create_ortho_sequences: 49 #if $create_ortho_sequences:
50 && echo "Sequences classified into pre-computed orthologous plant gene family clusters: `ls $src_dir | wc -l` files" > $output 50 && echo "Sequences classified into pre-computed orthologous plant gene family clusters: `ls $orthogroups_fasta_src_dir | wc -l` files" > $output
51 && mv $src_dir/* $dest_dir 51 && mv $orthogroups_fasta_src_dir/* $dest_dir
52 #end if 52 #end if
53 ]]> 53 ]]>
54 </command> 54 </command>
55 <inputs> 55 <inputs>
56 <param name="input" format="fasta" type="data" label="Amino acids (proteins) sequences fasta file"/> 56 <param name="input" format="fasta" type="data" label="Amino acids (proteins) sequences fasta file"/>
117 </conditional> 117 </conditional>
118 </when> 118 </when>
119 </conditional> 119 </conditional>
120 </inputs> 120 </inputs>
121 <outputs> 121 <outputs>
122 <data name="hmmscan_log" format="txt" label="Protein classification hmmscan.log on ${on_string}">
123 <filter>save_hmmscan_log_cond['classifier'] in ['hmmscan', 'both'] and save_hmmscan_log_cond['save_hmmscan_log'] == 'yes'</filter>
124 </data>
122 <data name="output" format="txt" label="Sequences classified into gene family clusters on ${on_string}"> 125 <data name="output" format="txt" label="Sequences classified into gene family clusters on ${on_string}">
123 <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes'</filter> 126 <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes'</filter>
124 </data>
125 <data name="hmmscan_log" format="txt" label="Protein classification hmmscan.log on ${on_string}">
126 <filter>save_hmmscan_log_cond['classifier'] in ['hmmscan', 'both'] and save_hmmscan_log_cond['save_hmmscan_log'] == 'yes'</filter>
127 </data> 127 </data>
128 <collection name="transcripts" type="list"> 128 <collection name="transcripts" type="list">
129 <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" /> 129 <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" />
130 </collection> 130 </collection>
131 </outputs> 131 </outputs>