Mercurial > repos > greg > phylogenomics_analysis

comparison phylogenomics_analysis.xml @ 4:37b56c1befaa draft

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author greg
date Thu, 05 Jan 2017 09:11:57 -0500
parents fd6773b7bb3f
children 26f5584ab88a
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3:fd6773b7bb3f 4:37b56c1befaa
62 #end if 62 #end if
63 #end if 63 #end if
64 #end if 64 #end if
65 #end if 65 #end if
66 --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds" 66 --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
67 --num_threads \${GALAXY_SLOTS:-4} && 67 --num_threads \${GALAXY_SLOTS:-4}
68 echo "Sequence alignments and corresponding phylogenies: `ls $src_dir | wc -l` files" > $output && 68 && echo "Sequence alignments and corresponding phylogenies: `ls $src_dir | wc -l` files" > $output
69 ls $src_dir >> $output && 69 && ls $src_dir >> $output
70 mv $src_dir/* $dest_dir 70 && mv $src_dir/* $dest_dir
71 ]]> 71 ]]>
72 </command> 72 </command>
73 <inputs> 73 <inputs>
74 <param name="orthogroup_fna" format="fasta" type="data" label="Gene family classification coding sequences (CDS) fasta file for which orthogroup fasta files were created"/> 74 <param name="orthogroup_fna" format="txt" type="data" label="Select sequences classified into gene family clusters"/>
75 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold"> 75 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
76 <options from_data_table="plant_tribes_scaffolds" /> 76 <options from_data_table="plant_tribes_scaffolds" />
77 <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."/> 77 <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."/>
78 </param> 78 </param>
79 <param name="method" type="select" label="Protein clustering method"> 79 <param name="method" type="select" label="Protein clustering method">