Mercurial > repos > greg > gene_family_classifier

comparison gene_family_classifier.xml @ 13:cddbb2f13c28 draft

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Uploaded
author greg
date Wed, 04 Jan 2017 14:14:27 -0500
parents b75510484c16
children 595088cc480a
comparison
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12:b75510484c16 13:cddbb2f13c28
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 #set create_ortho_sequences = 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 #if create_ortho_sequences:
17 #import os 16 #import os
17 #set create_ortho_sequences = True
18 #set src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta') 18 #set 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 $dest_dir &&
21 #else:
22 #set create_ortho_sequences = False
21 #end if 23 #end if
22 GeneFamilyClassifier 24 GeneFamilyClassifier
23 --proteins "$input" 25 --proteins "$input"
24 --scaffold "$scaffold" 26 --scaffold "$scaffold"
25 --method $method 27 --method $method
26 --classifier $classifier 28 --classifier $save_hmmscan_log_cond.classifier
27 #if str($options_type.options_type_selector) == 'advanced': 29 #if str($options_type.options_type_selector) == 'advanced':
28 --super_orthogroups $options_type.super_orthogroups 30 --super_orthogroups $options_type.super_orthogroups
29 #if str($options_type.single_copy_cond) == 'taxa': 31 #if str($options_type.single_copy_cond) == 'taxa':
30 --single_copy_taxa $options_type.single_copy_cond.single_copy_taxa 32 --single_copy_taxa $options_type.single_copy_cond.single_copy_taxa
31 --taxa_present $options_type.single_copy_cond.taxa_present 33 --taxa_present $options_type.single_copy_cond.taxa_present
35 --coding_sequences "$options_type.create_orthogroup_cond.coding_sequences" 37 --coding_sequences "$options_type.create_orthogroup_cond.coding_sequences"
36 #end if 38 #end if
37 #end if 39 #end if
38 --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds" 40 --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
39 --num_threads \${GALAXY_SLOTS:-4} 41 --num_threads \${GALAXY_SLOTS:-4}
40 #if str($classifier) == 'hmmscan' or str($classifier) == 'both': 42 #if str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both':
41 # Eliminate the hmmscan.log file 43 #if str($save_hmmscan_log_cond.save_hmmscan_log) == 'yes':
42 && rm $src_dir/*.log 44 && mv $src_dir/hmmscan.log $hmmscan_log
45 #else:
46 # Eliminate the hmmscan.log file
47 && rm $src_dir/hmmscan.log
48 #end if
43 #end if 49 #end if
44 #if create_ortho_sequences: 50 #if create_ortho_sequences:
45 && echo "Sequences classified into pre-computed orthologous plant gene family clusters: `ls $src_dir | wc -l` files" > $output 51 && echo "Sequences classified into pre-computed orthologous plant gene family clusters: `ls $src_dir | wc -l` files" > $output
46 && mv $src_dir/* $dest_dir 52 && mv $src_dir/* $dest_dir
47 #end if 53 #end if
56 <param name="method" type="select" label="Protein clustering method"> 62 <param name="method" type="select" label="Protein clustering method">
57 <option value="gfam" selected="true">GFam</option> 63 <option value="gfam" selected="true">GFam</option>
58 <option value="orthofinder">OrthoFinder</option> 64 <option value="orthofinder">OrthoFinder</option>
59 <option value="orthomcl">OrthoMCL</option> 65 <option value="orthomcl">OrthoMCL</option>
60 </param> 66 </param>
61 <param name="classifier" type="select" label="Protein classification method"> 67 <conditional name="save_hmmscan_log_cond">
62 <option value="blastp" selected="true">blastp</option> 68 <param name="classifier" type="select" label="Protein classification method">
63 <option value="hmmscan">HMMScan</option> 69 <option value="blastp" selected="true">blastp</option>
64 <option value="both">Both blastp and HMMScan</option> 70 <option value="hmmscan">HMMScan</option>
65 </param> 71 <option value="both">Both blastp and HMMScan</option>
72 </param>
73 <when value="blastp" />
74 <when value="hmmscan">
75 <param name="save_hmmscan_log" type="select" label="Save hmmscan log?" help="Save the hmmscan log in an additional output dataset">
76 <option value="no" selected="true">No</option>
77 <option value="yes">Yes</option>
78 </param>
79 </when>
80 <when value="both">
81 <param name="save_hmmscan_log" type="select" label="Save hmmscan log?" help="Save the hmmscan log in an additional output dataset">
82 <option value="no" selected="true">No</option>
83 <option value="yes">Yes</option>
84 </param>
85 </when>
86 </conditional>
66 <conditional name="options_type"> 87 <conditional name="options_type">
67 <param name="options_type_selector" type="select" label="Options Configuration"> 88 <param name="options_type_selector" type="select" label="Options Configuration">
68 <option value="basic" selected="true">Basic</option> 89 <option value="basic" selected="true">Basic</option>
69 <option value="advanced">Advanced</option> 90 <option value="advanced">Advanced</option>
70 </param> 91 </param>
99 </conditional> 120 </conditional>
100 </inputs> 121 </inputs>
101 <outputs> 122 <outputs>
102 <data name="output" format="txt" label="Sequences classified into gene family clusters on ${on_string}"> 123 <data name="output" format="txt" label="Sequences classified into gene family clusters on ${on_string}">
103 <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes'</filter> 124 <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes'</filter>
125 </data>
126 <data name="hmmscan_log" format="txt" label="Protein classification hmmscan.log on ${on_string}">
127 <filter>save_hmmscan_log_cond['classifier'] in ['hmmscan', 'both'] and save_hmmscan_log_cond['save_hmmscan_log'] == 'yes'</filter>
104 </data> 128 </data>
105 <collection name="transcripts" type="list"> 129 <collection name="transcripts" type="list">
106 <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" /> 130 <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" />
107 </collection> 131 </collection>
108 </outputs> 132 </outputs>