Mercurial > repos > brasset_jensen > srnapipe
changeset 30:b3f0209d3fec draft
Uploaded
| author | brasset_jensen |
|---|---|
| date | Sun, 27 May 2018 16:52:58 -0400 |
| parents | e10a2311e293 |
| children | 1198596f624f |
| files | sRNAPipe.xml |
| diffstat | 1 files changed, 244 insertions(+), 236 deletions(-) [+] |
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--- a/sRNAPipe.xml Sun May 27 16:52:04 2018 -0400 +++ b/sRNAPipe.xml Sun May 27 16:52:58 2018 -0400 @@ -1,236 +1,244 @@ -<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> +<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="0.7.12">bwa</requirement> + <requirement type="package" version="2.24">bedtools</requirement> + <requirement type="package" version="1.2">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> + <help> +<![CDATA[ +**User manual** +.. image:: sRNAPipe_User_Manual.pdf +@REFERENCES@ +]]> + + </help> +</tool>