Mercurial > repos > jjohnson > transindel
comparison transindel.xml @ 3:eddf2f556a92 draft default tip
"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 |
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| 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"> |