Mercurial > repos > galaxyp > translate_bed_sequences
changeset 1:6bbce76c78c1 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 7025b29e8113049e5f21389ce67858c18af6611b
| author | galaxyp |
|---|---|
| date | Thu, 15 Dec 2016 18:41:21 -0500 |
| parents | d723eb657f1d |
| children | 4221664a2bd0 |
| files | tool_dependencies.xml translate_bed_sequences.xml |
| diffstat | 2 files changed, 116 insertions(+), 125 deletions(-) [+] |
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--- a/tool_dependencies.xml Mon Jan 25 12:21:21 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="biopython" version="1.62"> - <repository changeset_revision="f06c96348778" name="package_biopython_1_62" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>
--- a/translate_bed_sequences.xml Mon Jan 25 12:21:21 2016 -0500 +++ b/translate_bed_sequences.xml Thu Dec 15 18:41:21 2016 -0500 @@ -1,121 +1,118 @@ -<?xml version="1.0"?> -<tool id="translate_bed_sequences" name="Translate BED Sequences" version="0.1.0"> - <description>3 frame translation of BED augmented with a sequence column</description> - <requirements> - <requirement type="package" version="1.62">biopython</requirement> - <requirement type="python-module">Bio</requirement> - </requirements> - <command interpreter="python"> - translate_bed_sequences.py --input "$input" - #if $fa_db: - --fa_db='$fa_db' - #end if - #if $fa_sep: - --fa_sep='$fa_sep' - #end if - #if $id_prefix: - --id_prefix='$id_prefix' - #end if - #if $reference: - --reference $reference - #else: - --reference ${input.metadata.dbkey} - #end if - #if $refsource: - --refsource $refsource - #end if - #if $seqtype: - --seqtype $seqtype - #end if - #if $score_name: - --score_name $score_name - #end if - #if $filter.filterseqs == 'yes': - #if $filter.leading_bp: - --leading_bp $filter.leading_bp - #end if - #if $filter.trailing_bp: - --trailing_bp $filter.trailing_bp - #end if - #else: - --unfiltered - #end if - #if $trim.trimseqs == 'no': - --untrimmed - #if str($trim.max_stop_codons) != '': - --max_stop_codons $trim.max_stop_codons - #end if - #end if - #if str($min_length) != '': - --min_length $min_length - #end if - --bed $translated_bed - --output "$output" - </command> - <inputs> - <param name="input" type="data" format="bed" label="BED file with added sequence column" - help="Output from 'Extract Genomic DNA' run on tophat junctions.bed "/> - <param name="fa_db" type="text" value="" optional="true" label="fasta ID source, e.g. generic" - help="Any Compomics application such as PeptideShaker, requires a source"> - </param> - <param name="fa_sep" type="text" value="" optional="true" label="fasta ID line separator character" - help="Only used when a fasta ID source is given, defaults to the pipe character"> - </param> - <param name="id_prefix" type="text" value="" optional="true" label="ID prefix for generated IDs" - help="Can be used to distinguish samples"> - <validator type="regex" message="Allowed chars:a-z A-Z 0-9 _ - |">^[a-zA-Z0-9_-|]*$</validator> - </param> - <param name="refsource" type="text" value="Ensembl" optional="true" label="Genome reference source" - help=""/> - <param name="reference" type="text" value="" optional="true" label="Genome reference name" - help="By default, the database metadata will be used."/> - <param name="seqtype" type="text" value="" optional="true" label="The SEQTYPE:STATUS to include in the fasta ID lines" - help="For example: pep:splice"/> - <param name="score_name" type="text" value="" optional="true" label="Add the bed score field fasta ID line with this tag name" - help="For example: with the tag name 'depth' and bed score 12: depth:12"/> - <conditional name="filter"> - <param name="filterseqs" type="select" label="Filter out translations with stop codons before the splice site"> - <option value="yes" selected="true">Yes</option> - <option value="no">No</option> - </param> - <when value="yes"> - <param name="leading_bp" type="integer" value="" min="0" optional="true" label="Stop codon filtering start position base pairs" - help="Do not reject translation is stop_codons are within base pairs of the BED start position for positive strand"/> - <param name="trailing_bp" type="integer" value="" min="0" optional="true" label="Stop codon filtering end position base pairs" - help="Do not reject translation is stop_codons are within base pairs of the BED end position for negative strand"/> - </when> - <when value="no"/> - </conditional> - <conditional name="trim"> - <param name="trimseqs" type="select" label="Trim translations to stop codons"> - <option value="yes" selected="true">Yes</option> - <option value="no">No</option> - </param> - <when value="no"> - <param name="max_stop_codons" type="integer" value="" min="0" optional="true" label="Maximum number of stop codons allowed in a translation to be reported"/> - </when> - </conditional> - <param name="min_length" type="integer" value="" min="0" optional="true" label="Minimum length of a translation to be reported"/> - </inputs> - <stdio> - <exit_code range="1:" level="fatal" description="Error" /> - </stdio> - <outputs> - <data name="translated_bed" metadata_source="input" format="bed" label="${tool.name} on ${on_string} bed"> - </data> - <data name="output" metadata_source="input" format="fasta" label="${tool.name} on ${on_string} fasta"> - </data> - </outputs> - <tests> - <test> - <param name="input" value="Extract_Genomic_DNA.bed" ftype="bed" dbkey="hg19"/> - <param name="reference" value="GRCh37"/> - <param name="seqtype" value="pep:novel"/> - <param name="score_name" value="depth"/> - <output name="output" file="translated_bed_sequences.fa"/> - </test> - </tests> - <help> +<tool id="translate_bed_sequences" name="Translate BED Sequences" version="0.1.1"> + <description>3 frame translation of BED augmented with a sequence column</description> + <requirements> + <requirement type="package" version="1.62">biopython</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + <command> + python '$__tool_directory__/translate_bed_sequences.py' + --input '$input' + #if $fa_db: + --fa_db='$fa_db' + #end if + #if $fa_sep: + --fa_sep='$fa_sep' + #end if + #if $id_prefix: + --id_prefix='$id_prefix' + #end if + #if $reference: + --reference $reference + #else: + --reference ${input.metadata.dbkey} + #end if + #if $refsource: + --refsource $refsource + #end if + #if $seqtype: + --seqtype $seqtype + #end if + #if $score_name: + --score_name $score_name + #end if + #if $filter.filterseqs == 'yes': + #if $filter.leading_bp: + --leading_bp $filter.leading_bp + #end if + #if $filter.trailing_bp: + --trailing_bp $filter.trailing_bp + #end if + #else: + --unfiltered + #end if + #if $trim.trimseqs == 'no': + --untrimmed + #if str($trim.max_stop_codons) != '': + --max_stop_codons $trim.max_stop_codons + #end if + #end if + #if str($min_length) != '': + --min_length $min_length + #end if + --bed $translated_bed + --output '$output' + </command> + <inputs> + <param name="input" type="data" format="bed" label="BED file with added sequence column" + help="Output from 'Extract Genomic DNA' run on tophat junctions.bed "/> + <param name="fa_db" type="text" value="" optional="true" label="fasta ID source, e.g. generic" + help="Any Compomics application such as PeptideShaker, requires a source"> + </param> + <param name="fa_sep" type="text" value="" optional="true" label="fasta ID line separator character" + help="Only used when a fasta ID source is given, defaults to the pipe character"> + </param> + <param name="id_prefix" type="text" value="" optional="true" label="ID prefix for generated IDs" + help="Can be used to distinguish samples"> + <validator type="regex" message="Allowed chars:a-z A-Z 0-9 _ - |">^[a-zA-Z0-9_-|]*$</validator> + </param> + <param name="refsource" type="text" value="Ensembl" optional="true" label="Genome reference source" + help=""/> + <param name="reference" type="text" value="" optional="true" label="Genome reference name" + help="By default, the database metadata will be used."/> + <param name="seqtype" type="text" value="" optional="true" label="The SEQTYPE:STATUS to include in the fasta ID lines" + help="For example: pep:splice"/> + <param name="score_name" type="text" value="" optional="true" label="Add the bed score field fasta ID line with this tag name" + help="For example: with the tag name 'depth' and bed score 12: depth:12"/> + <conditional name="filter"> + <param name="filterseqs" type="select" label="Filter out translations with stop codons before the splice site"> + <option value="yes" selected="true">Yes</option> + <option value="no">No</option> + </param> + <when value="yes"> + <param name="leading_bp" type="integer" value="" min="0" optional="true" label="Stop codon filtering start position base pairs" + help="Do not reject translation is stop_codons are within base pairs of the BED start position for positive strand"/> + <param name="trailing_bp" type="integer" value="" min="0" optional="true" label="Stop codon filtering end position base pairs" + help="Do not reject translation is stop_codons are within base pairs of the BED end position for negative strand"/> + </when> + <when value="no"/> + </conditional> + <conditional name="trim"> + <param name="trimseqs" type="select" label="Trim translations to stop codons"> + <option value="yes" selected="true">Yes</option> + <option value="no">No</option> + </param> + <when value="no"> + <param name="max_stop_codons" type="integer" value="" min="0" optional="true" label="Maximum number of stop codons allowed in a translation to be reported"/> + </when> + </conditional> + <param name="min_length" type="integer" value="" min="0" optional="true" label="Minimum length of a translation to be reported"/> + </inputs> + <outputs> + <data name="translated_bed" metadata_source="input" format="bed" label="${tool.name} on ${on_string} bed" /> + <data name="output" metadata_source="input" format="fasta" label="${tool.name} on ${on_string} fasta" /> + </outputs> + <tests> + <test> + <param name="input" value="Extract_Genomic_DNA.bed" ftype="bed" dbkey="hg19"/> + <param name="reference" value="GRCh37"/> + <param name="seqtype" value="pep:novel"/> + <param name="score_name" value="depth"/> + <output name="output" file="translated_bed_sequences.fa"/> + </test> + </tests> + <help> **Translate BED Sequences** This tool takes a BED input file that has been processed @@ -124,5 +121,5 @@ It generates a peptide fasta file with the 3-frame translations of the spliced sequence defined by each entry in the input BED file. - </help> + </help> </tool>