Mercurial > repos > brasset_jensen > srnapipe
changeset 69:fa794d2a5aaf draft
planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit bd03f99240a3d174c1b22245fbdf45e15edb4a5e
| author | brasset_jensen |
|---|---|
| date | Tue, 12 Feb 2019 04:11:07 -0500 |
| parents | a5a99218ef7a |
| children | be25d16676f6 |
| files | sRNAPipe.xml |
| diffstat | 1 files changed, 174 insertions(+), 124 deletions(-) [+] |
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--- a/sRNAPipe.xml Wed Feb 06 04:03:15 2019 -0500 +++ b/sRNAPipe.xml Tue Feb 12 04:11:07 2019 -0500 @@ -1,14 +1,14 @@ <tool id="sRNAPipe" name="sRNAPipe" version="1.1"> <description>In-depth study of small RNA</description> <macros> - <xml name="source" token_arg="Argument" token_build="Build argument"> + <xml name="source" token_arg="Argument" token_build="Build argument" token_ref=""> <conditional name="source"> - <param name="source" type="select" label="Will you select the database from your history or use a built-in index?"> + <param name="source" type="select" label="Will you select the reference 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@"> + <param name="indices" argument="@ARG@" type="select" label="Select @REF@"> <options from_data_table="bwa_indexes"> <filter type="sort_by" column="2" /> <validator type="no_options" message="No indexes are available" /> @@ -16,146 +16,186 @@ </param> </when> <when value="history"> - <param name="file" argument="@ARG@" type="data" format="fasta" label="Select a reference from history" /> + <param name="file" argument="@ARG@" type="data" format="fasta" label="Select @REF@ from history" help="We will also use @BUILD@"/> </when> </conditional> </xml> + <xml name="conditional_source" token_arg="Argument" token_build="Build argument" token_ref="" token_name=""> + <conditional name="@NAME@"> + <param name="use_ref" type="select" label="Use @REF@?"> + <option value="true">Yes</option> + <option value="false" selected="true">No</option> + </param> + <when value="true"> + <expand macro="source" arg="@ARG@" build="@BUILD@" ref="@REF@"/> + </when> + <when value="false"/> + </conditional> + </xml> </macros> <requirements> <requirement type="package" version="1.1">srnapipe</requirement> </requirements> <version_command>srnapipe | grep 'version' | grep "version" | cut -d ' ' -f 3</version_command> <command detect_errors="aggressive"><![CDATA[ - srnapipe - - --fastq '${first_input}' - --fastq_n '${first_input.name}' - #for $input_file in $input_files: - --fastq '${input_file.additional_input}' - --fastq_n '${input_file.additional_input.name}' +srnapipe + #if str($inputs.custom) == 'true' + #for $x in $inputs.inputs + --fastq '$x.fastq' + --fastq_n '$x.fastq_n' #end for - - #if $genome.source.source == "history": - --ref '${genome.source.file}' - --build_index - #else: - --ref '${genome.source.indices.fields.path}' - #end if + #else + #for $x in $inputs.fastq + --fastq '$x' + --fastq_n '$x.element_identifier' + #end for + #end if + --min $min + --max $max - #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 $genome.source.source == "history" + --ref '$genome.source.file' + --build_index + #else + --ref '$genome.source.indices.fields.path' + #end if + --mis $genome.mis - #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 $transcripts.source.source == "history" + --transcripts '$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 + --misTE $te.misTE - #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}' + #if $mirnas.source.source == "history" + --miRNAs '$mirnas.source.file' + --build_miRNAs + #else: + --miRNAs '$mirnas.source.indices.fields.path' + #end if + + #if str($snrnas.snrnas.use_ref) == 'true' + #if str($snrnas.snrnas.source.source) == "history" + --snRNAs '$snrnas.snrnas.source.file' + --build_snRNAs + #else + --snRNAs '$snrnas.snrnas.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 + #else + --snRNAs "None" + #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 '${TE.source.indices.fields.path}' + #if str($rrnas.rrnas.use_ref) == 'true' + #if str($rrnas.rrnas.source.source) == "history" + --rRNAs '$rrnas.rrnas.source.file' + --build_rRNAs + #else + --rRNAs '$rrnas.rrnas.source.indices.fields.path' #end if + #else + --rRNAs "None" + #end if - --si_min $si_min - --si_max $si_max - --pi_min $pi_min - --pi_max $pi_max - --min $min - --max $max + #if str($trnas.trnas.use_ref) == 'true' + #if str($trnas.trnas.source.source) == "history" + --tRNAs '$trnas.trnas.source.file' + --build_tRNAs + #else + --tRNAs '$trnas.trnas.source.indices.fields.path' + #end if + #else + --tRNAs "None" + #end if - --mis $mis - --misTE $misTE - --dir $html_out.files_path - --html $html_out - --PPPon $PPPon + --si_min $sirna.si_min + --si_max $sirna.si_max + --pi_min $pirna.pi_min + --pi_max $pirna.pi_max + --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> + <conditional name="inputs"> + <param name="custom" type="select" label="Use custom name for the input sequence files?"> + <option value="true">Yes</option> + <option value="false" selected="true">No: the names will be extracted automatically</option> + </param> + <when value="true"> + <repeat name="inputs" title="Input sequences" min="1"> + <param argument="--fastq" type="data" format="fastqsanger" label="Input sequences"/> + <param argument="--fastq_n" type="text" value="" label="Label for the input sequences"/> + </repeat> + </when> + <when value="false"> + <param argument="--fastq" type="data" format="fastqsanger" multiple="true" label="Input sequences" help="Also set a name with --fastq_n"/> + </when> + </conditional> + <param argument="--min" type="integer" value="18" label="Minimum read size"/> + <param argument="--max" type="integer" value="29" label="Maximum read size"/> <section name="genome" title="Reference genome" expanded="true"> - <expand macro="source" arg="--ref" build="--build_index"/> + <expand macro="source" arg="--ref" build="--build_index" ref="a reference genome"/> + <param argument="--mis" type="integer" value="0" label="Maximal genome mismatches"/> </section> <section name="transcripts" title="Transcripts" expanded="true"> - <expand macro="source" arg="--transcripts" build="--build_transcripts"/> + <expand macro="source" arg="--transcripts" build="--build_transcripts" ref="reference transcript sequences"/> </section> - <section name="TE" title="Transposable Elements" expanded="true"> - <expand macro="source" arg="--TE" build="--build_TE"/> + <section name="te" title="Transposable Elements" expanded="true"> + <expand macro="source" arg="--TE" build="--build_TE" ref="reference TE sequences"/> + <param argument="--misTE" type="integer" value="3" label="maximal TE mismatches"/> </section> - <section name="miRNAs" title="miRNAs" expanded="true"> - <expand macro="source" arg="--miRNAs" build="--build_miRNAs"/> + <section name="mirnas" title="miRNAs" expanded="true"> + <expand macro="source" arg="--miRNAs" build="--build_miRNAs" ref="reference miRNAs sequences"/> </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 name="snrnas" title="snRNAs" expanded="true"> + <expand macro="conditional_source" name="snrnas" arg="--snRNAs" build="--build_snRNAs" ref="reference snRNAs sequences"/> </section> - <section name="tRNAs" title="tRNAs" expanded="true"> - <expand macro="source" arg="--tRNAs" build="--build_tRNAs"/> + <section name="rrnas" title="rRNAs" expanded="true"> + <expand macro="conditional_source" name="rrnas" arg="--rRNAs" build="--build_rRNAs" ref="reference rRNAs sequences"/> + </section> + <section name="trnas" title="tRNAs" expanded="true"> + <expand macro="conditional_source" name="trnas" arg="--tRNAs" build="--build_tRNAs" ref="reference tRNAs sequences"/> </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"/> + <section name="sirna" title="siRNA" expanded="true"> + <param argument="--si_min" type="integer" value="21" label="Lower bound for siRNA range"/> + <param argument="--si_max" type="integer" value="21" label="Higher bound of siRNA range"/> + </section> + <section name="pirna" title="piRNA" expanded="true"> + <param argument="--pi_min" type="integer" value="23" label="lower bound of piRNA range"/> + <param argument="--pi_max" type="integer" value="29" label="higher bound of piRNA range"/> + </section> + <param name="PPPon" argument="--PPPon" type="boolean" truevalue="true" falsevalue="false" 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="${tool.name}_fastq_outputs" name="output_fastqsanger"> + <data format="html" name="html_out" label="${tool.name} on ${on_string}: HTML report"/> + <collection type="list" label="${tool.name} on ${on_string}: 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" /> + <conditional name="inputs"> + <param name="custom" value="false"/> + <param name="fastq" value="reads-sample-small.fastq"/> + </conditional> + <param name="min" value="18" /> + <param name="max" value="29" /> <section name="genome"> <conditional name="source"> <param name="source" value="history" /> <param name="file" value ="genome-small.fa" /> </conditional> + <param name="mis" value="0" /> </section> <section name="transcripts"> <conditional name="source"> @@ -163,44 +203,54 @@ <param name="file" value ="transcripts-file-small.fa" /> </conditional> </section> - <section name="TE"> + <section name="te"> <conditional name="source"> <param name="source" value="history" /> <param name="file" value ="TE-file-small.fa" /> </conditional> + <param name="misTE" value="3" /> </section> - <section name="miRNAs"> + <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" /> + <section name="snrnas"> + <conditional name="snrnas"> + <param name="use_ref" value="true"/> + <conditional name="source"> + <param name="source" value="history" /> + <param name="file" value ="dmel-all-sn-snoRNA-r6.03.fasta" /> + </conditional> </conditional> </section> - <section name="rRNAs"> - <conditional name="source"> - <param name="source" value="history" /> - <param name="file" value ="dmel-all-rRNA-r6.03.fasta" /> + <section name="rrnas"> + <conditional name="rrnas"> + <param name="use_ref" value="true"/> + <conditional name="source"> + <param name="source" value="history" /> + <param name="file" value ="dmel-all-rRNA-r6.03.fasta" /> + </conditional> </conditional> </section> - <section name="tRNAs"> - <conditional name="source"> - <param name="source" value="history" /> - <param name="file" value ="dmel-all-tRNA-r6.03.fasta" /> + <section name="trnas"> + <conditional name="trnas"> + <param name="use_ref" value="true"/> + <conditional name="source"> + <param name="source" value="history" /> + <param name="file" value ="dmel-all-tRNA-r6.03.fasta" /> + </conditional> </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" /> + <section name="sirna"> + <param name="si_min" value="21" /> + <param name="si_max" value="21" /> + </section> + <section name="pirna"> + <param name="pi_min" value="23" /> + <param name="pi_max" value="29" /> + </section> <param name="PPPon" value="true" /> <output name='html_out' file="res.html" compare='diff' lines_diff = '10'/> <output_collection name="output_fastqsanger" type="list">