Mercurial > repos > greg > plant_tribes_gene_family_aligner

comparison gene_family_aligner.xml @ 7:2ac7090847f9 draft

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Uploaded
author greg
date Thu, 21 Dec 2017 09:14:22 -0500
parents 3384b6a842b0
children 32587f12102c
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6:3384b6a842b0 7:2ac7090847f9
45 #if str($remove_sequences_with_gaps_cond.iterative_realignment): 45 #if str($remove_sequences_with_gaps_cond.iterative_realignment):
46 --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment 46 --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment
47 #end if 47 #end if
48 #end if 48 #end if
49 #end if 49 #end if
50 &>proc.log 50 &>gene_family_aligner_log.txt;
51 if [[ $? -ne 0 ]]; then
52 find geneFamilyAlignments_dir -type d -maxdepth 1 -exec cp gene_family_aligner_log.txt {} \;
53 exit 1;
54 fi
51 ]]></command> 55 ]]></command>
52 <inputs> 56 <inputs>
53 <param name="input" format="fasta" type="data_collection" collection_type="list" label="Integrated orthogroup fasta files" /> 57 <param name="input" format="fasta" type="data_collection" collection_type="list" label="Integrated orthogroup fasta files" />
54 <conditional name="alignment_method_cond"> 58 <conditional name="alignment_method_cond">
55 <param name="alignment_method" type="select" force_select="true" label="Multiple sequence alignment method"> 59 <param name="alignment_method" type="select" force_select="true" label="Multiple sequence alignment method">
127 </collection> 131 </collection>
128 <collection name="filtered_fna" type="list" label="${tool.name} (filtered orthogroup codon alignments) on ${on_string}"> 132 <collection name="filtered_fna" type="list" label="${tool.name} (filtered orthogroup codon alignments) on ${on_string}">
129 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_filtered_aln_fna" format="fasta" /> 133 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_filtered_aln_fna" format="fasta" />
130 <filter>codon_alignments == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter> 134 <filter>codon_alignments == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
131 </collection> 135 </collection>
132
133 </outputs> 136 </outputs>
134 <tests> 137 <tests>
135 <test> 138 <test>
136 <param name="input"> 139 <param name="input">
137 <collection type="list"> 140 <collection type="list">