Mercurial > repos > greg > gene_family_classifier

comparison gene_family_classifier.xml @ 9:c7010d37df2c draft

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author greg
date Wed, 04 Jan 2017 10:07:01 -0500
parents d678d4c2e9e1
children fe24cd3bf71a
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8:d678d4c2e9e1 9:c7010d37df2c
10 <regex match="Error:" /> 10 <regex match="Error:" />
11 <regex match="Exception:" /> 11 <regex match="Exception:" />
12 </stdio> 12 </stdio>
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 #set create_ortho_sequences = str($options_type.options_type_selector) == 'advanced' and str($options_type.create_orthogroup_cond.create_orthogroup) == 'yes'
16 #if create_ortho_sequences:
16 #import os 17 #import os
17 #set orthogroups_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta') 18 #set src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
18 #set orthogroups_dest_dir = $options_type.create_orthogroup_cond.coding_sequences.extra_files_path 19 #set dest_dir = $output.extra_files_path
19 mkdir -p $orthogroups_dest_dir && 20 mkdir -p $dest_dir &&
20 #end if 21 #end if
21 GeneFamilyClassifier 22 GeneFamilyClassifier
22 --proteins "$input" 23 --proteins "$input"
23 --scaffold "$scaffold" 24 --scaffold "$scaffold"
24 --method $method 25 --method $method
34 --coding_sequences "$options_type.create_orthogroup_cond.coding_sequences" 35 --coding_sequences "$options_type.create_orthogroup_cond.coding_sequences"
35 #end if 36 #end if
36 #end if 37 #end if
37 --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds" 38 --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
38 --num_threads \${GALAXY_SLOTS:-4} 39 --num_threads \${GALAXY_SLOTS:-4}
39 #if str($options_type.options_type_selector) == 'advanced' and str($options_type.create_orthogroup_cond.create_orthogroup) == 'yes': 40 #if create_ortho_sequences:
40 && mv $orthogroups_src_dir/* $orthogroups_dest_dir 41 echo "Sequences classified into pre-computed orthologous plant gene family clusters: `ls $src_dir | wc -l` files" > $output &&
42 && mv $src_dir/* $dest_dir
41 #end if 43 #end if
42 ]]> 44 ]]>
43 </command> 45 </command>
44 <inputs> 46 <inputs>
45 <param name="input" format="fasta" type="data" label="Amino acids (proteins) sequences fasta file"/> 47 <param name="input" format="fasta" type="data" label="Amino acids (proteins) sequences fasta file"/>
91 </conditional> 93 </conditional>
92 </when> 94 </when>
93 </conditional> 95 </conditional>
94 </inputs> 96 </inputs>
95 <outputs> 97 <outputs>
98 <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>
100 </data>
96 <collection name="transcripts" type="list"> 101 <collection name="transcripts" type="list">
97 <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="true" ext="fasta" /> 102 <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" />
98 </collection> 103 </collection>
99 </outputs> 104 </outputs>
100 <tests> 105 <tests>
101 <test> 106 <test>
102 <param name="input" value="" ftype="fasta" /> 107 <param name="input" value="" ftype="fasta" />
110 </output_collection> 115 </output_collection>
111 </test> 116 </test>
112 </tests> 117 </tests>
113 <help> 118 <help>
114 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of 119 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of
115 complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It performs Gene family 120 complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It performs gene family
116 classification of the post processed de novo transcripts using either blastp (faster), HMMScan (slower but more sensitive to remote 121 classification of the post processed de novo transcripts using either blastp (faster), HMMScan (slower but more sensitive to remote
117 homologs) or both (more exhaustive). 122 homologs) or both (more exhaustive).
118 123
119 ----- 124 -----
120 125