Mercurial > repos > greg > assembly_post_processor

comparison assembly_post_processor.xml @ 102:62df33ce7eaa draft

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Uploaded
author greg
date Thu, 07 Dec 2017 15:23:07 -0500
parents 7ca8ab9a46e9
children 6b071ce71267
comparison
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101:7ca8ab9a46e9 102:62df33ce7eaa
33 #end if 33 #end if
34 --min_length $options_type.min_length 34 --min_length $options_type.min_length
35 #end if 35 #end if
36 --num_threads \${GALAXY_SLOTS:-4} 36 --num_threads \${GALAXY_SLOTS:-4}
37 &>proc.log 37 &>proc.log
38 && if [[ $? -ne 0 ]]; then
39 exec &>/dev/tty;
40 cat proc.log >&2;
41 fi
38 && mv $output_dir/transcripts.cds '$output_cds' 42 && mv $output_dir/transcripts.cds '$output_cds'
39 && mv $output_dir/transcripts.pep '$output_pep' 43 && mv $output_dir/transcripts.pep '$output_pep'
40 && mv $output_dir/transcripts.cleaned.cds '$output_cleaned_cds' 44 && mv $output_dir/transcripts.cleaned.cds '$output_cleaned_cds'
41 && mv $output_dir/transcripts.cleaned.pep '$output_cleaned_pep' 45 && mv $output_dir/transcripts.cleaned.pep '$output_cleaned_pep'
42 #if str($options_type.options_type_selector) == 'advanced': 46 #if str($options_type.options_type_selector) == 'advanced':
46 #if str($options_type.dereplicate) == 'yes': 50 #if str($options_type.dereplicate) == 'yes':
47 && mv $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds' 51 && mv $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds'
48 && mv $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep' 52 && mv $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep'
49 #end if 53 #end if
50 #end if 54 #end if
51 && if [[ $? -ne 0 ]]; then
52 cat proc.log >&2;
53 fi
54 ]]></command> 55 ]]></command>
55 <inputs> 56 <inputs>
56 <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/> 57 <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/>
57 <conditional name="prediction_method_cond"> 58 <conditional name="prediction_method_cond">
58 <param name="prediction_method" type="select" label="Coding regions prediction method"> 59 <param name="prediction_method" type="select" label="Coding regions prediction method">