Mercurial > repos > brasset_jensen > srnapipe
view sRNAPipe.xml @ 26:b3be854a4273 draft
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author | brasset_jensen |
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date | Sun, 20 May 2018 16:55:31 -0400 |
parents | 9f6ece278d09 |
children | b3f0209d3fec |
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<tool id="sRNAPipe" name="sRNAPipe" version="0.0.1"> <description>In-depth study of small RNA</description> <command interpreter="perl"> ./bin/sRNAPipe.pl --fastq ${first_input} --fastq_n ${first_input.name} #for $input_file in $input_files: --fastq ${input_file.additional_input} --fastq_n ${input_file.additional_input.name} #end for #if $Genome.refGenomeSource == "history": --ref "${Genome.ownFile}" --build_index #else: --ref "${Genome.indices.fields.path}" #end if #if $tRNAs.refGenomeSource == "history": --tRNAs "${tRNAs.ownFile}" --build_tRNAs #elif $tRNAs.refGenomeSource == "none": --tRNAs "None" #else: --tRNAs "${tRNAs.indices.fields.path}" #end if #if $snRNAs.refGenomeSource == "history": --snRNAs "${snRNAs.ownFile}" --build_snRNAs #elif $snRNAs.refGenomeSource == "none": --snRNAs "None" #else: --snRNAs "${snRNAs.indices.fields.path}" #end if #if $rRNAs.refGenomeSource == "history": --rRNAs "${rRNAs.ownFile}" --build_rRNAs #elif $rRNAs.refGenomeSource == "none": --rRNAs "None" #else: --rRNAs "${rRNAs.indices.fields.path}" #end if #if $miRNAs.refGenomeSource == "history": --miRNAs "${miRNAs.ownFile}" --build_miRNAs #else: --miRNAs "${miRNAs.indices.fields.path}" #end if #if $transcripts.refGenomeSource == "history": --transcripts "${transcripts.ownFile}" --build_transcripts #else: --transcripts "${transcripts.indices.fields.path}" #end if #if $TE.refGenomeSource == "history": --TE "${TE.ownFile}" --build_TE #else: --TE "${TE.indices.fields.path}" #end if --si_min $si_min --si_max $si_max --pi_min $pi_min --pi_max $pi_max --min $min --max $max --mis $mis --misTE $misTE --dir $html_out.files_path --html $html_out --PPPon $PPPon </command> <requirements> <requirement type="package" version="0.7.15">bwa</requirement> <requirement type="package" version="2.26.0">bedtools</requirement> <requirement type="package" version="1.5">samtools</requirement> </requirements> <inputs> <param format="fastqsanger" name="first_input" type="data" label="fastqsanger (Q33)" help=""/> <repeat name="input_files" title="Additional Fastq Files"> <param format="fastqsanger" name="additional_input" type="data" label="fastqsanger (Q33)" help=""/> </repeat> <conditional name="Genome"> <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?"> <option value="indexed">Use a built-in index</option> <option value="history">Use one from the history</option> </param> <when value="indexed"> <param name="indices" type="select" label="Select a reference genome"> <options from_data_table="bwa_indexes"> <filter type="sort_by" column="2" /> <validator type="no_options" message="No indexes are available" /> </options> </param> </when> <when value="history"> <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> </when> </conditional> <conditional name="transcripts"> <param name="refGenomeSource" type="select" label="Will you select transcripts database from your history or use a built-in index?"> <option value="indexed">Use a built-in index</option> <option value="history">Use one from the history</option> </param> <when value="indexed"> <param name="indices" type="select" label="Select a transcripts reference"> <options from_data_table="bwa_indexes"> <filter type="sort_by" column="2" /> <validator type="no_options" message="No indexes are available" /> </options> </param> </when> <when value="history"> <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> </when> </conditional> <conditional name="TE"> <param name="refGenomeSource" type="select" label="Will you select TE database from your history or use a built-in index?"> <option value="indexed">Use a built-in index</option> <option value="history">Use one from the history</option> </param> <when value="indexed"> <param name="indices" type="select" label="Select a TE reference"> <options from_data_table="bwa_indexes"> <filter type="sort_by" column="2" /> <validator type="no_options" message="No indexes are available" /> </options> </param> </when> <when value="history"> <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> </when> </conditional> <conditional name="miRNAs"> <param name="refGenomeSource" type="select" label="Will you select miRNA database from your history or use a built-in index?"> <option value="indexed">Use a built-in index</option> <option value="history">Use one from the history</option> </param> <when value="indexed"> <param name="indices" type="select" label="Select a miRNA reference"> <options from_data_table="bwa_indexes"> <filter type="sort_by" column="2" /> <validator type="no_options" message="No indexes are available" /> </options> </param> </when> <when value="history"> <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> </when> </conditional> <conditional name="snRNAs"> <param name="refGenomeSource" type="select" label="Will you select snRNA database from your history or use a built-in index?"> <option value="indexed">Use a built-in index</option> <option value="history">Use one from the history</option> <option value="none">None</option> </param> <when value="indexed"> <param name="indices" type="select" label="Select a snRNAs reference"> <options from_data_table="bwa_indexes"> <filter type="sort_by" column="2" /> <validator type="no_options" message="No indexes are available" /> </options> </param> </when> <when value="history"> <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> </when> </conditional> <conditional name="rRNAs"> <param name="refGenomeSource" type="select" label="Will you select rRNAs database from your history or use a built-in index?"> <option value="indexed">Use a built-in index</option> <option value="history">Use one from the history</option> <option value="none">None</option> </param> <when value="indexed"> <param name="indices" type="select" label="Select a rRNAs reference"> <options from_data_table="bwa_indexes"> <filter type="sort_by" column="2" /> <validator type="no_options" message="No indexes are available" /> </options> </param> </when> <when value="history"> <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> </when> </conditional> <conditional name="tRNAs"> <param name="refGenomeSource" type="select" label="Will you select tRNA database from your history or use a built-in index?"> <option value="indexed">Use a built-in index</option> <option value="history">Use one from the history</option> <option value="none">None</option> </param> <when value="indexed"> <param name="indices" type="select" label="Select a tRNA reference"> <options from_data_table="bwa_indexes"> <filter type="sort_by" column="2" /> <validator type="no_options" message="No indexes are available" /> </options> </param> </when> <when value="history"> <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> </when> </conditional> <param name="min" type="integer" value="18" label="minimum read size"/> <param name="max" type="integer" value="29" label="maximum read size"/> <param name="si_min" type="integer" value="21" label="lower bound of siRNA range"/> <param name="si_max" type="integer" value="21" label="higher bound of siRNA range"/> <param name="pi_min" type="integer" value="23" label="lower bound of piRNA range"/> <param name="pi_max" type="integer" value="29" label="higher bound of piRNA range"/> <param name="mis" type="integer" value="0" label="maximal genome mismatches"/> <param name="misTE" type="integer" value="3" label="maximal TE mismatches"/> <param name="PPPon" type="boolean" checked="true" label="PPPartners"/> </inputs> <outputs> <data format="html" name="html_out" label="${tool.name}_${first_input.name}_${on_string}"/> <collection format ="fastqsanger" type="list" label="${tool.name}_fastq_outputs" name="output_fastqsanger"> <discover_datasets format ="fastqsanger" pattern="(?P<name>.*)" directory="fastq_dir" /> </collection> </outputs> </tool>