Mercurial > repos > greg > gene_family_classifier

comparison gene_family_classifier.xml @ 39:c4f809cd2f38 draft

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Uploaded
author greg
date Mon, 06 Feb 2017 09:04:44 -0500
parents b63f96ff6708
children 6cf0fff77dea
comparison
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38:b63f96ff6708 39:c4f809cd2f38
11 <regex match="Error:" /> 11 <regex match="Error:" />
12 <regex match="Exception:" /> 12 <regex match="Exception:" />
13 </stdio> 13 </stdio>
14 <command> 14 <command>
15 <![CDATA[ 15 <![CDATA[
16 #import os 16 #import os
17 #set scaffold_path = $scaffold.fields.path 17 #set scaffold_path = $scaffold.fields.path
18 #set scaffold_dir = $os.path.split($scaffold_path)[0] 18 #set scaffold_dir = $os.path.split($scaffold_path)[0]
19 #set scaffold_selection = $os.path.split($scaffold_path)[1] 19 #set scaffold_selection = $os.path.split($scaffold_path)[1]
20 20
21 #if str($options_type.options_type_selector) == 'advanced': 21 #if str($options_type.options_type_selector) == 'advanced':
22 #set create_orthogroup_cond = $options_type.create_orthogroup_cond 22 #set create_orthogroup_cond = $options_type.create_orthogroup_cond
23 #set create_orthogroup = $create_orthogroup_cond.create_orthogroup 23 #set create_orthogroup = $create_orthogroup_cond.create_orthogroup
24 24
31 #end if 31 #end if
32 32
33 #set create_ortho_sequences = True 33 #set create_ortho_sequences = True
34 #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta') 34 #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
35 #if $create_corresponding_coding_sequences: 35 #if $create_corresponding_coding_sequences:
36 #set dest_dir = $output_ptcgfcs.extra_files_path 36 #set dest_dir = $output_ptcgfcs.extra_files_path
37 #else: 37 #else:
38 #set dest_dir = $output_ptcgf.extra_files_path 38 #set dest_dir = $output_ptcgf.extra_files_path
39 #end if 39 #end if
40 mkdir -p $dest_dir && 40 mkdir -p $dest_dir &&
41 #else: 41 #else:
42 #set create_ortho_sequences = False 42 #set create_ortho_sequences = False
43 #set create_corresponding_coding_sequences = False 43 #set create_corresponding_coding_sequences = False
44 #end if 44 #end if
77 #end if 77 #end if
78 #end if 78 #end if
79 79
80 #if $create_ortho_sequences: 80 #if $create_ortho_sequences:
81 #if $create_corresponding_coding_sequences: 81 #if $create_corresponding_coding_sequences:
82 && echo "# Precomputed orthologous gene family clusters with corresponding coding sequences: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output_ptcgfcs 82 && echo '#Precomputed orthologous gene family clusters with corresponding coding sequences: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files' > $output_ptcgfcs
83 && ls -al $orthogroups_fasta_src_dir | grep f >> $output_ptcgfcs 83 && echo '#Size File' > $output_ptcgfcs
84 && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_ptcgfcs
84 #else: 85 #else:
85 && echo "# Precomputed orthologous gene family clusters: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output_ptcgf 86 && echo '#Precomputed orthologous gene family clusters: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files' > $output_ptcgf
86 && ls -al $orthogroups_fasta_src_dir | grep f >> $output_ptcgf 87 && echo '#Size File' > $output_ptcgf
88 && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_ptcgf
87 #end if 89 #end if
88 && mv $orthogroups_fasta_src_dir/* $dest_dir || true 90 && mv $orthogroups_fasta_src_dir/* $dest_dir || true
89 #end if 91 #end if
90 92
91 ]]> 93 ]]>
92 </command> 94 </command>
93 <inputs> 95 <inputs>
94 <param name="input" format="fasta" type="data" label="Amino acids (proteins) sequences fasta file"/> 96 <param name="input" format="fasta" type="data" label="Amino acids (proteins) sequences fasta file"/>
95 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold"> 97 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
96 <options from_data_table="plant_tribes_scaffolds" /> 98 <options from_data_table="plant_tribes_scaffolds" />
97 <validator type="no_options" message="No PlantTribes scaffolds are available. Use the PlantTribes Scaffolds Download Data Manager tool to install and populate the PlantTribes scaffolds data table."/> 99 <validator type="no_options" message="No PlantTribes scaffolds are available. Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table."/>
98 </param> 100 </param>
99 <param name="method" type="select" label="Protein clustering method"> 101 <param name="method" type="select" label="Protein clustering method">
100 <option value="gfam" selected="true">GFam</option> 102 <option value="gfam" selected="true">GFam</option>
101 <option value="orthofinder">OrthoFinder</option> 103 <option value="orthofinder">OrthoFinder</option>
102 <option value="orthomcl">OrthoMCL</option> 104 <option value="orthomcl">OrthoMCL</option>
178 <collection name="orthos" type="list"> 180 <collection name="orthos" type="list">
179 <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" /> 181 <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" />
180 </collection> 182 </collection>
181 </outputs> 183 </outputs>
182 <tests> 184 <tests>
183 <!-- Not sure how to test this since the tool requires scaffolds data which is extremely large and installed using a Data Manager --> 185 <!-- Not sure how to test this since the tool requires scaffolds data which is extremely large and installed using a Data Manager -->
184 <!-- 186 <!--
185 <test> 187 <test>
186 <param name="input" value="transcripts.cleaned.nr.pep" ftype="fasta" /> 188 <param name="input" value="transcripts.cleaned.nr.pep" ftype="fasta" />
187 <param name="scaffold" value="22Gv1.1"/> 189 <param name="scaffold" value="22Gv1.1"/>
188 <param name="method" value="orthomcl"/> 190 <param name="method" value="orthomcl"/>
189 <param name="classifier" value="blastp"/> 191 <param name="classifier" value="blastp"/>