Mercurial > repos > brasset_jensen > srnapipe
diff sRNAPipe.xml @ 61:9185ca0a7b43 draft
Updated package according to recommendations.
| author | pierre.pouchin |
|---|---|
| date | Wed, 16 Jan 2019 08:18:13 -0500 |
| parents | 9645d995fb3c |
| children | e6c4f3e96e47 |
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--- a/sRNAPipe.xml Wed Oct 24 07:40:20 2018 -0400 +++ b/sRNAPipe.xml Wed Jan 16 08:18:13 2019 -0500 @@ -1,252 +1,271 @@ -<tool id="sRNAPipe" name="sRNAPipe" version="1.0"> - <description>In-depth study of small RNA</description> - <command><![CDATA[ - perl '$__tool_directory__/bin/sRNAPipe.pl' - - --fastq '${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="0.7.12">bwa</requirement> - <requirement type="package" version="2.24">bedtools</requirement> - <requirement type="package" version="1.5">samtools</requirement> - <requirement type="package" version="3.3.2">r-base</requirement> - <requirement type="package" version="5.22.0">perl</requirement> - <requirement type="package" version="2.50">perl-getopt-long</requirement> - <requirement type="package" version="1.17">perl-parallel-forkmanager</requirement> - <requirement type="package" version="0.34" >perl-statistics-r</requirement> - <requirement type="package" version="0.30">perl-string-random</requirement> - <requirement type="package" version="0.38" >perl-file-copy-recursive</requirement> - <requirement type="package" version="0.1" >perl-math-cdf</requirement> - <requirement type="package" version="3.6">r-plotrix</requirement> - <requirement type="package" version="1.14.0">bioconductor-sushi</requirement> - <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement> - <requirement type="package" version="2.2.1">r-ggplot2</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> - <help> - **User manual** - "https://github.com/brassetjensen/sRNAPipe/blob/master/sRNAPipe_User_Manual.pdf" - </help> -</tool> +<tool id="sRNAPipe" name="sRNAPipe" version="1.1"> + <description>In-depth study of small RNA</description> + <macros> + <xml name="source"> + <conditional name="source"> + <param name="source" type="select" label="Will you select the 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" argument="@ARG@" type="select" label="Select a reference genome" help="Also use @BUILD@"> + <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="file" argument="@ARG@" type="data" format="fasta" label="Select a reference from history" /> + </when> + </conditional> + </xml> + </macros> + <requirements> + <requirement type="package" version="0.7.12">bwa</requirement> + <requirement type="package" version="2.24">bedtools</requirement> + <requirement type="package" version="1.5">samtools</requirement> + <requirement type="package" version="3.3.2">r-base</requirement> + <requirement type="package" version="5.22.0">perl</requirement> + <requirement type="package" version="2.50">perl-getopt-long</requirement> + <requirement type="package" version="1.17">perl-parallel-forkmanager</requirement> + <requirement type="package" version="0.34" >perl-statistics-r</requirement> + <requirement type="package" version="0.30">perl-string-random</requirement> + <requirement type="package" version="0.38" >perl-file-copy-recursive</requirement> + <requirement type="package" version="0.1" >perl-math-cdf</requirement> + <requirement type="package" version="3.6">r-plotrix</requirement> + <requirement type="package" version="1.14.0">bioconductor-sushi</requirement> + <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement> + <requirement type="package" version="2.2.1">r-ggplot2</requirement> + </requirements> + <version_command>perl '$__tool_directory__/bin/sRNAPipe.pl'</version_command> + <command detect_errors="aggressive"><![CDATA[ + perl '$__tool_directory__/bin/sRNAPipe.pl' + + --fastq '${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 $genome.source.source == "history": + --ref '${genome.source.file}' + --build_index + #else: + --ref '${genome.source.indices.fields.path}' + #end if + + #if $tRNAs.source.source == "history": + --tRNAs '${tRNAs.source.file}' + --build_tRNAs + #elif $tRNAs.source.source == "none": + --tRNAs "None" + #else: + --tRNAs '${tRNAs.source.indices.fields.path}' + #end if + + #if $snRNAs.source.source == "history": + --snRNAs '${snRNAs.source.file}' + --build_snRNAs + #elif $snRNAs.source.source == "none": + --snRNAs "None" + #else: + --snRNAs '${snRNAs.source.indices.fields.path}' + #end if + + #if $rRNAs.source.source == "history": + --rRNAs '${rRNAs.source.file}' + --build_rRNAs + #elif $rRNAs.source.source == "none": + --rRNAs "None" + #else: + --rRNAs '${rRNAs.source.indices.fields.path}' + #end if + + #if $miRNAs.source.source == "history": + --miRNAs '${miRNAs.source.file}' + --build_miRNAs + #else: + --miRNAs '${miRNAs.source.indices.fields.path}' + #end if + + #if $transcripts.source.source == "history": + --transcripts '${transcripts.source.file}' + --build_transcripts + #else: + --transcripts '${transcripts.source.indices.fields.path}' + #end if + + #if $TE.source.source == "history": + --TE '${TE.source.file}' + --build_TE + #else: + --TE '${TE.source.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> + + <inputs> + <param name="first_input" argument="--fastq" type="data" format="fastqsanger" label="fastqsanger (Q33)" help="Also set a name with --fastq_n"/> + <repeat name="input_files" title="Additional Fastq Files"> + <param name="additional_input" argument="--fastq" type="data" format="fastqsanger" label="fastqsanger (Q33)" help="Also set a name after each fastq with --fastq_n"/> + </repeat> + <section name="genome" title="Reference genome" expanded="true"> + <expand macro="source" arg="--ref" build="--build_index"/> + </section> + <section name="transcripts" title="Transcripts" expanded="true"> + <expand macro="source" arg="--transcripts" build="--build_transcripts"/> + </section> + <section name="TE" title="Transposable Elements" expanded="true"> + <expand macro="source" arg="--TE" build="--build_TE"/> + </section> + <section name="miRNAs" title="miRNAs" expanded="true"> + <expand macro="source" arg="--miRNAs" build="--build_miRNAs"/> + </section> + <section name="snRNAs" title="snRNAs" expanded="true"> + <expand macro="source" arg="--snRNAs" build="--build_snRNAs"/> + </section> + <section name="rRNAs" title="rRNAs" expanded="true"> + <expand macro="source" arg="--rRNAs" build="--build_rRNAs"/> + </section> + <section name="tRNAs" title="tRNAs" expanded="true"> + <expand macro="source" arg="--tRNAs" build="--build_tRNAs"/> + </section> + + <param name="min" argument="--min" type="integer" value="18" label="minimum read size"/> + <param name="max" argument="--max" type="integer" value="29" label="maximum read size"/> + <param name="si_min" argument="--si_min" type="integer" value="21" label="lower bound of siRNA range"/> + <param name="si_max" argument="--si_max" type="integer" value="21" label="higher bound of siRNA range"/> + <param name="pi_min" argument="--pi_min" type="integer" value="23" label="lower bound of piRNA range"/> + <param name="pi_max" argument="--pi_max" type="integer" value="29" label="higher bound of piRNA range"/> + <param name="mis" argument="--mis" type="integer" value="0" label="maximal genome mismatches"/> + <param name="misTE" argument="--misTE" type="integer" value="3" label="maximal TE mismatches"/> + <param name="PPPon" argument="--PPPon" type="boolean" checked="true" label="PPPartners"/> + </inputs> + <outputs> + <data format="html" name="html_out" label="${tool.name} on ${first_input.name} (${on_string}): HTML report"/> + <collection type="list" label="${tool.name}_fastq_outputs" name="output_fastqsanger"> + <discover_datasets format ="fastqsanger" pattern="__designation_and_ext__" directory="fastq_dir" /> + </collection> + </outputs> + <tests> + <test> + <param name="first_input" value="reads-sample-small.fastq" /> + <section name="genome"> + <conditional name="source"> + <param name="source" value="history" /> + <param name="file" value ="genome-small.fa" /> + </conditional> + </section> + <section name="transcripts"> + <conditional name="source"> + <param name="source" value="history" /> + <param name="file" value ="transcripts-file-small.fa" /> + </conditional> + </section> + <section name="TE"> + <conditional name="source"> + <param name="source" value="history" /> + <param name="file" value ="TE-file-small.fa" /> + </conditional> + </section> + <section name="miRNAs"> + <conditional name="source"> + <param name="source" value="history" /> + <param name="file" value ="mirbase-21-dme-hairpins-16jul2015.fa" /> + </conditional> + </section> + <section name="snRNAs"> + <conditional name="source"> + <param name="source" value="history" /> + <param name="file" value ="dmel-all-sn-snoRNA-r6.03.fasta" /> + </conditional> + </section> + <section name="rRNAs"> + <conditional name="source"> + <param name="source" value="history" /> + <param name="file" value ="dmel-all-rRNA-r6.03.fasta" /> + </conditional> + </section> + <section name="tRNAs"> + <conditional name="source"> + <param name="source" value="history" /> + <param name="file" value ="dmel-all-tRNA-r6.03.fasta" /> + </conditional> + </section> + <param name="min" value="18" /> + <param name="max" value="29" /> + <param name="si_min" value="21" /> + <param name="si_max" value="21" /> + <param name="pi_min" value="23" /> + <param name="pi_max" value="29" /> + <param name="mis" value="0" /> + <param name="misTE" value="3" /> + <param name="PPPon" value="true" /> + <output name='html_out' file="res.html" compare='diff' lines_diff = '10'/> + <output_collection name="output_fastqsanger" type="list"> + <element name="reads-sample-small.fastq_all_mappers" file="fastq_dir/reads-sample-small.fastq_all_mappers.fastq" /> + <element name="reads-sample-small.fastq-bonafide_reads-genome" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-genome.fastq" /> + <element name="reads-sample-small.fastq-bonafide_reads-genome_uni" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-genome_uni.fastq" /> + <element name="reads-sample-small.fastq-bonafide_reads-TEs" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-TEs.fastq" /> + <element name="reads-sample-small.fastq-bonafide_reads-TEs_uni" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-TEs_uni.fastq" /> + <element name="reads-sample-small.fastq-bonafide_reads-transcripts" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-transcripts.fastq" /> + <element name="reads-sample-small.fastq-bonafide_reads-transcripts_uni" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-transcripts_uni.fastq" /> + <element name="reads-sample-small.fastq-miRNAs-genome" file="fastq_dir/reads-sample-small.fastq-miRNAs-genome.fastq" /> + <element name="reads-sample-small.fastq-miRNAs-genome_uni" file="fastq_dir/reads-sample-small.fastq-miRNAs-genome_uni.fastq" /> + <element name="reads-sample-small.fastq-miRNAs-TEs_uni" file="fastq_dir/reads-sample-small.fastq-miRNAs-TEs_uni.fastq" /> + <element name="reads-sample-small.fastq-miRNAs-transcripts" file="fastq_dir/reads-sample-small.fastq-miRNAs-transcripts.fastq" /> + <element name="reads-sample-small.fastq-miRNAs-transcripts_uni" file="fastq_dir/reads-sample-small.fastq-miRNAs-transcripts_uni.fastq" /> + <element name="reads-sample-small.fastq-piRNAs-genome" file="fastq_dir/reads-sample-small.fastq-piRNAs-genome.fastq" /> + <element name="reads-sample-small.fastq-piRNAs-genome_uni" file="fastq_dir/reads-sample-small.fastq-piRNAs-genome_uni.fastq" /> + <element name="reads-sample-small.fastq-piRNAs-TEs" file="fastq_dir/reads-sample-small.fastq-piRNAs-TEs.fastq" /> + <element name="reads-sample-small.fastq-piRNAs-TEs_uni" file="fastq_dir/reads-sample-small.fastq-piRNAs-TEs_uni.fastq" /> + <element name="reads-sample-small.fastq-piRNAs-transcripts" file="fastq_dir/reads-sample-small.fastq-piRNAs-transcripts.fastq" /> + <element name="reads-sample-small.fastq-piRNAs-transcripts_uni" file="fastq_dir/reads-sample-small.fastq-piRNAs-transcripts_uni.fastq" /> + <element name="reads-sample-small.fastq-siRNAs-genome" file="fastq_dir/reads-sample-small.fastq-siRNAs-genome.fastq" /> + <element name="reads-sample-small.fastq-siRNAs-genome_uni" file="fastq_dir/reads-sample-small.fastq-siRNAs-genome_uni.fastq" /> + <element name="reads-sample-small.fastq-siRNAs-TEs" file="fastq_dir/reads-sample-small.fastq-siRNAs-TEs.fastq" /> + <element name="reads-sample-small.fastq-siRNAs-TEs_uni" file="fastq_dir/reads-sample-small.fastq-siRNAs-TEs_uni.fastq" /> + <element name="reads-sample-small.fastq-siRNAs-transcripts" file="fastq_dir/reads-sample-small.fastq-siRNAs-transcripts.fastq" /> + <element name="reads-sample-small.fastq-siRNAs-transcripts_uni" file="fastq_dir/reads-sample-small.fastq-siRNAs-transcripts_uni.fastq" /> + <element name="reads-sample-small.fastq_unique_mappers" file="fastq_dir/reads-sample-small.fastq_unique_mappers.fastq" /> + <element name="reads-sample-small.fastq_unmapped" file="fastq_dir/reads-sample-small.fastq_unmapped.fastq" /> + </output_collection> + </test> + </tests> + <help> + **User manual** + "https://github.com/brassetjensen/sRNAPipe/blob/master/sRNAPipe_User_Manual.pdf" + </help> + <citations> + <citation type="doi">10.1038/nature12962</citation> + <citation type="doi">10.1038/nature11233</citation> + <citation type="doi">10.1186/gb4172</citation> + <citation type="doi">10.1038/nature04916</citation> + <citation type="doi">10.1016/j.cell.2007.01.043</citation> + <citation type="doi">10.1016/j.celrep.2015.02.062</citation> + <citation type="doi">10.1093/bioinformatics/btp324</citation> + <citation type="doi">10.1093/bioinformatics/btp352</citation> + <citation type="doi">10.1002/0471250953.bi1112s47</citation> + <citation type="doi">10.1093/bioinformatics/btu379</citation> + <citation type="doi">10.1002/embr.201337898</citation> + <citation type="doi">10.1038/ncomms13739</citation> + <citation type="doi">10.1093/nar/gkt310</citation> + <citation type="doi">10.1186/s13072-015-0041-5</citation> + <citation type="doi">10.1093/bioinformatics/btu647</citation> + </citations> +</tool>