Mercurial > repos > jjohnson > transindel

comparison transindel.xml @ 3:eddf2f556a92 draft default tip

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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/transindel commit af32e767fd29667d3e29f1a202ad59d3dd498c84-dirty"
author jjohnson
date Mon, 30 Mar 2020 22:06:19 -0400
parents ba3910d7bd99
children
comparison
equal deleted inserted replaced
2:42d0c1c21cd4 3:eddf2f556a92
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="version_command" /> 7 <expand macro="version_command" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 ln -s -f '${analyze.input}' 'input.bam' &&
10 ln -s -f '${analyze.input.metadata.bam_index}' 'input.bai' &&
9 #if $analyze.input_src == 'RNA' 11 #if $analyze.input_src == 'RNA'
10 #if $analyze.rfasta.rfasta_source == "history": 12 #if $analyze.rfasta.rfasta_source == "history":
11 ln -s '$analyze.rfasta.ref_fa_hist' ref.fa && 13 ln -s '$analyze.rfasta.ref_fa_hist' ref.fa &&
12 #else: 14 #else:
13 ln -s '$analyze.rfasta.ref_fa_builtin.fields.path' ref.fa && 15 ln -s '$analyze.rfasta.ref_fa_builtin.fields.path' ref.fa &&
14 #end if 16 #end if
15 transIndel_build_RNA.py -i '$analyze.input' -o 'transIndel.bam' 17 transIndel_build_RNA.py -i 'input.bam' -o 'transIndel.bam'
16 ## Get reference FASTA 18 ## Get reference FASTA
17 -r ref.fa 19 -r ref.fa
18 ## Get reference GTF 20 ## Get reference GTF
19 #if $analyze.rgtf.rgtf_source == "history": 21 #if $analyze.rgtf.rgtf_source == "history":
20 -g '$analyze.rgtf.ref_gtf_hist' 22 -g '$analyze.rgtf.ref_gtf_hist'
34 #if $analyze.transIndel_call.call_opts.regions.regions_source != 'none': 36 #if $analyze.transIndel_call.call_opts.regions.regions_source != 'none':
35 -t '$analyze.transIndel_call.call_opts.regions.target' 37 -t '$analyze.transIndel_call.call_opts.regions.target'
36 #end if 38 #end if
37 #end if 39 #end if
38 #elif $analyze.input_src == 'DNA' 40 #elif $analyze.input_src == 'DNA'
39 transIndel_build_DNA.py -i '$analyze.input' -o 'transIndel.bam' 41 transIndel_build_DNA.py -i 'input.bam' -o 'transIndel.bam'
40 --mapq_cutoff $analyze.mapq_cutoff 42 --mapq_cutoff $analyze.mapq_cutoff
41 --max_del_length $analyze.max_del_length 43 --max_del_length $analyze.max_del_length
42 #if $analyze.transIndel_call.run_transIndel_call == 'yes' 44 #if $analyze.transIndel_call.run_transIndel_call == 'yes'
43 #if $analyze.rfasta.rfasta_source == "history": 45 #if $analyze.rfasta.rfasta_source == "history":
44 && ln -s '$analyze.transIndel_call.rfasta.ref_fa_hist' ref.fa 46 && ln -s '$analyze.transIndel_call.rfasta.ref_fa_hist' ref.fa
60 #if $analyze.rfasta.rfasta_source == "history": 62 #if $analyze.rfasta.rfasta_source == "history":
61 ln -s '$analyze.rfasta.ref_fa_hist' ref.fa && 63 ln -s '$analyze.rfasta.ref_fa_hist' ref.fa &&
62 #else: 64 #else:
63 ln -s '$analyze.rfasta.ref_fa_builtin.fields.path' ref.fa && 65 ln -s '$analyze.rfasta.ref_fa_builtin.fields.path' ref.fa &&
64 #end if 66 #end if
65 transIndel_call.py -i '$analyze.input' -o 'transIndel' 67 transIndel_call.py -i 'input.bam' -o 'transIndel'
66 -r re.fasta 68 -r ref.fa
67 -c $analyze.call_opts.min_observation_count 69 -c $analyze.call_opts.min_observation_count
68 -d $analyze.call_opts.min_depth 70 -d $analyze.call_opts.min_depth
69 -f $analyze.call_opts.min_allele_frequency 71 -f $analyze.call_opts.min_allele_frequency
70 -l $analyze.call_opts.min_length 72 -l $analyze.call_opts.min_length
71 -m $analyze.call_opts.min_mapq 73 -m $analyze.call_opts.min_mapq
103 </when> 105 </when>
104 </conditional> 106 </conditional>
105 </inputs> 107 </inputs>
106 <outputs> 108 <outputs>
107 <data name="output_bam" format="bam" label="${tool.name} on ${on_string}: transIndel.bam" from_work_dir="transIndel.bam"> 109 <data name="output_bam" format="bam" label="${tool.name} on ${on_string}: transIndel.bam" from_work_dir="transIndel.bam">
108 <filter>analyze['input_src'] != 'transindel' </filter> 110 <filter>analyze['input_src'] != 'transIndel'</filter>
109 </data> 111 </data>
110 <data name="output_vcf" format="vcf" label="${tool.name} on ${on_string}: transIndel.indel.vcf" from_work_dir="transIndel.indel.vcf" > 112 <data name="output_vcf" format="vcf" label="${tool.name} on ${on_string}: transIndel.indel.vcf" from_work_dir="transIndel.indel.vcf" >
111 <filter>analyze['input_src'] == 'transindel' or analyze['transIndel_call']['run_transIndel_call'] == 'yes'</filter> 113 <filter>analyze['input_src'] == 'transIndel' or analyze['transIndel_call']['run_transIndel_call'] == 'yes'</filter>
112 </data> 114 </data>
113 </outputs> 115 </outputs>
114 <tests> 116 <tests>
115 <test> 117 <test>
116 <conditional name="analyze"> 118 <conditional name="analyze">