Mercurial > repos > jjohnson > transindel
diff transindel.xml @ 0:ba3910d7bd99 draft
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/transindel commit f102f45fafcda3ee868765784d2f69d2dcad6233-dirty"
| author | jjohnson |
|---|---|
| date | Fri, 27 Mar 2020 10:01:26 -0400 |
| parents | |
| children | eddf2f556a92 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/transindel.xml Fri Mar 27 10:01:26 2020 -0400 @@ -0,0 +1,139 @@ +<tool id="transindel" name="transIndel" version="@VERSION@.0" python_template_version="3.5"> + <description>detect indels from RNAseq or DNAseq BWA-MEM mapping</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + <command detect_errors="exit_code"><![CDATA[ + #if $analyze.input_src == 'RNA' + #if $analyze.rfasta.rfasta_source == "history": + ln -s '$analyze.rfasta.ref_fa_hist' ref.fa && + #else: + ln -s '$analyze.rfasta.ref_fa_builtin.fields.path' ref.fa && + #end if + transIndel_build_RNA.py -i '$analyze.input' -o 'transIndel.bam' + ## Get reference FASTA + -r ref.fa + ## Get reference GTF + #if $analyze.rgtf.rgtf_source == "history": + -g '$analyze.rgtf.ref_gtf_hist' + #else: + -g '$analyze.rgtf.ref_gtf_builtin.fields.path' + #end if + --mapq_cutoff $analyze.mapq_cutoff + --max_del_length $analyze.max_del_length + #if $analyze.transIndel_call.run_transIndel_call == 'yes' + && transIndel_call.py -i 'transIndel.bam' -o transIndel + -r ref.fa + -c $analyze.transIndel_call.call_opts.min_observation_count + -d $analyze.transIndel_call.call_opts.min_depth + -f $analyze.transIndel_call.call_opts.min_allele_frequency + -l $analyze.transIndel_call.call_opts.min_length + -m $analyze.transIndel_call.call_opts.min_mapq + #if $analyze.transIndel_call.call_opts.regions.regions_source != 'none': + -t '$analyze.transIndel_call.call_opts.regions.target' + #end if + #end if + #elif $analyze.input_src == 'DNA' + transIndel_build_DNA.py -i '$analyze.input' -o 'transIndel.bam' + --mapq_cutoff $analyze.mapq_cutoff + --max_del_length $analyze.max_del_length + #if $analyze.transIndel_call.run_transIndel_call == 'yes' + #if $analyze.rfasta.rfasta_source == "history": + && ln -s '$analyze.transIndel_call.rfasta.ref_fa_hist' ref.fa + #else: + && ln -s '$analyze.transIndel_call.rfasta.ref_fa_builtin.fields.path' ref.fa + #end if + && transIndel_call.py -i 'transIndel.bam' -o transIndel + -r ref.fa + -c $analyze.transIndel_call.call_opts.min_observation_count + -d $analyze.transIndel_call.call_opts.min_depth + -f $analyze.transIndel_call.call_opts.min_allele_frequency + -l $analyze.transIndel_call.call_opts.min_length + -m $analyze.transIndel_call.call_opts.min_mapq + #if $analyze.transIndel_call.call_opts.regions.regions_source != 'none': + -t '$analyze.transIndel_call.call_opts.regions.target' + #end if + #end if + #elif $analyze.input_src == 'transIndel' + #if $analyze.rfasta.rfasta_source == "history": + ln -s '$analyze.rfasta.ref_fa_hist' ref.fa && + #else: + ln -s '$analyze.rfasta.ref_fa_builtin.fields.path' ref.fa && + #end if + transIndel_call.py -i '$analyze.input' -o 'transIndel' + -r re.fasta + -c $analyze.call_opts.min_observation_count + -d $analyze.call_opts.min_depth + -f $analyze.call_opts.min_allele_frequency + -l $analyze.call_opts.min_length + -m $analyze.call_opts.min_mapq + #if $analyze.call_opts.regions.regions_source != 'none': + -t '$analyze.call_opts.regions.target' + #end if + #end if + ]]></command> + <inputs> + <conditional name="analyze"> + <param name="input_src" type="select" label=""> + <option value="RNA">RNA bwa-mem bam</option> + <option value="DNA">DNA bwa-mem bam</option> + <option value="transIndel">transIndel bam</option> + </param> + <when value="RNA"> + <param name="input" type="data" format="bam" label="bwa-mem bam from RNAseq data"/> + <expand macro="reference_genome"/> + <expand macro="reference_gtf"/> + <param name="splice_site_half_bin_size" argument="-s" type="integer" value="20" min="0" label="splice site half bin size" help="(splice site half bin size)"/> + <expand macro="build_opts" token_default_mapq_cutoff="60"/> + <expand macro="transindel_call"/> + </when> + <when value="DNA"> + <param name="input" type="data" format="bam" label="bwa-mem bam from DNAseq data"/> + <expand macro="build_opts" token_default_mapq_cutoff="15"/> + <expand macro="transindel_call"> + <expand macro="reference_genome"/> + </expand> + </when> + <when value="transIndel"> + <param name="input" type="data" format="bam" label="transIndel bam"/> + <expand macro="reference_genome"/> + <expand macro="call_opts"/> + </when> + </conditional> + </inputs> + <outputs> + <data name="output_bam" format="bam" label="${tool.name} on ${on_string}: transIndel.bam" from_work_dir="transIndel.bam"> + <filter>analyze['input_src'] != 'transindel' </filter> + </data> + <data name="output_vcf" format="vcf" label="${tool.name} on ${on_string}: transIndel.indel.vcf" from_work_dir="transIndel.indel.vcf" > + <filter>analyze['input_src'] == 'transindel' or analyze['transIndel_call']['run_transIndel_call'] == 'yes'</filter> + </data> + </outputs> + <tests> + <test> + <conditional name="analyze"> + <param name="input_src" value="RNA"/> + <param name="input" ftype="bam" value="RNA.bam"/> + <conditional name="rfasta"> + <param name="rfasta_source" value="history"/> + <param name="ref_fa_hist" ftype="fasta" value="GRCh38_20.fa" /> + </conditional> + <conditional name="rgtf"> + <param name="rgtf_source" value="history"/> + <param name="ref_gtf_hist" ftype="gtf" value="GRCh38_20.gtf" /> + </conditional> + </conditional> + <output name="output_vcf"> + <assert_contents> + <has_text text="SVTYPE=DEL" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + TODO: Fill in help. + ]]></help> + <expand macro="citations" /> +</tool>