| Previous changeset 0:d723eb657f1d (2016-01-25) Next changeset 2:4221664a2bd0 (2020-04-07) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 7025b29e8113049e5f21389ce67858c18af6611b |
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modified:
translate_bed_sequences.xml |
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removed:
tool_dependencies.xml |
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| diff -r d723eb657f1d -r 6bbce76c78c1 tool_dependencies.xml --- a/tool_dependencies.xml Mon Jan 25 12:21:21 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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> |
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| diff -r d723eb657f1d -r 6bbce76c78c1 translate_bed_sequences.xml --- 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 |
| [ |
| b'@@ -1,121 +1,118 @@\n-<?xml version="1.0"?>\n-<tool id="translate_bed_sequences" name="Translate BED Sequences" version="0.1.0">\n- <description>3 frame translation of BED augmented with a sequence column</description>\n- <requirements>\n- <requirement type="package" version="1.62">biopython</requirement>\n- <requirement type="python-module">Bio</requirement>\n- </requirements>\n- <command interpreter="python">\n- translate_bed_sequences.py --input "$input" \n- #if $fa_db:\n- --fa_db=\'$fa_db\'\n- #end if\n- #if $fa_sep:\n- --fa_sep=\'$fa_sep\'\n- #end if\n- #if $id_prefix:\n- --id_prefix=\'$id_prefix\'\n- #end if\n- #if $reference:\n- --reference $reference\n- #else:\n- --reference ${input.metadata.dbkey}\n- #end if\n- #if $refsource:\n- --refsource $refsource\n- #end if\n- #if $seqtype:\n- --seqtype $seqtype\n- #end if\n- #if $score_name:\n- --score_name $score_name\n- #end if\n- #if $filter.filterseqs == \'yes\':\n- #if $filter.leading_bp:\n- --leading_bp $filter.leading_bp\n- #end if\n- #if $filter.trailing_bp:\n- --trailing_bp $filter.trailing_bp\n- #end if\n- #else:\n- --unfiltered\n- #end if\n- #if $trim.trimseqs == \'no\':\n- --untrimmed\n- #if str($trim.max_stop_codons) != \'\':\n- --max_stop_codons $trim.max_stop_codons\n- #end if\n- #end if\n- #if str($min_length) != \'\':\n- --min_length $min_length \n- #end if\n- --bed $translated_bed\n- --output "$output"\n- </command>\n- <inputs>\n- <param name="input" type="data" format="bed" label="BED file with added sequence column" \n- help="Output from \'Extract Genomic DNA\' run on tophat junctions.bed "/> \n- <param name="fa_db" type="text" value="" optional="true" label="fasta ID source, e.g. generic"\n- help="Any Compomics application such as PeptideShaker, requires a source">\n- </param>\n- <param name="fa_sep" type="text" value="" optional="true" label="fasta ID line separator character"\n- help="Only used when a fasta ID source is given, defaults to the pipe character">\n- </param>\n- <param name="id_prefix" type="text" value="" optional="true" label="ID prefix for generated IDs"\n- help="Can be used to distinguish samples">\n- <validator type="regex" message="Allowed chars:a-z A-Z 0-9 _ - |">^[a-zA-Z0-9_-|]*$</validator>\n- </param>\n- <param name="refsource" type="text" value="Ensembl" optional="true" label="Genome reference source"\n- help=""/>\n- <param name="reference" type="text" value="" optional="true" label="Genome reference name"\n- help="By default, the database metadata will be used."/>\n- <param name="seqtype" type="text" value="" optional="true" label="The SEQTYPE:STATUS to include in the fasta ID lines"\n- help="For example: pep:splice"/>\n- <param name="score_name" type="text" value="" optional="true" label="Add the bed score field fasta ID line with this tag name"\n- help="For example: with the tag name \'depth\' and bed score 12: depth:12"/>\n- <conditional name="filter">\n- <param name="filterseqs" type="select" label="Filter out translations with stop codons before the splice site">\n- <option value="yes" selected="true">Yes</option>\n- <option value="no">No</option>\n- </param>\n- <when value="yes">\n- <param name="leading_bp" type="integer" value="" min="0" optional="true" label="Stop codon filtering start position base pairs" \n- help="Do not reject translation is stop_codons are within base pairs of the BED start position for positive strand"/>\n- <param name="trailing_bp" type="integer" value="" min="0" optional="true" label="Stop codon filtering end position base pairs" \n- help="Do not reject translation is stop_codons are within base pairs of the BED end position for negative strand"/>\n- </when>\n- <when value="no"/>\n- </conditional>\n- <conditional name="trim">\n- <param name="trimseqs" type="select" label="Trim translations to st'..b'tophat junctions.bed "/> \n+ <param name="fa_db" type="text" value="" optional="true" label="fasta ID source, e.g. generic"\n+ help="Any Compomics application such as PeptideShaker, requires a source">\n+ </param>\n+ <param name="fa_sep" type="text" value="" optional="true" label="fasta ID line separator character"\n+ help="Only used when a fasta ID source is given, defaults to the pipe character">\n+ </param>\n+ <param name="id_prefix" type="text" value="" optional="true" label="ID prefix for generated IDs"\n+ help="Can be used to distinguish samples">\n+ <validator type="regex" message="Allowed chars:a-z A-Z 0-9 _ - |">^[a-zA-Z0-9_-|]*$</validator>\n+ </param>\n+ <param name="refsource" type="text" value="Ensembl" optional="true" label="Genome reference source"\n+ help=""/>\n+ <param name="reference" type="text" value="" optional="true" label="Genome reference name"\n+ help="By default, the database metadata will be used."/>\n+ <param name="seqtype" type="text" value="" optional="true" label="The SEQTYPE:STATUS to include in the fasta ID lines"\n+ help="For example: pep:splice"/>\n+ <param name="score_name" type="text" value="" optional="true" label="Add the bed score field fasta ID line with this tag name"\n+ help="For example: with the tag name \'depth\' and bed score 12: depth:12"/>\n+ <conditional name="filter">\n+ <param name="filterseqs" type="select" label="Filter out translations with stop codons before the splice site">\n+ <option value="yes" selected="true">Yes</option>\n+ <option value="no">No</option>\n+ </param>\n+ <when value="yes">\n+ <param name="leading_bp" type="integer" value="" min="0" optional="true" label="Stop codon filtering start position base pairs" \n+ help="Do not reject translation is stop_codons are within base pairs of the BED start position for positive strand"/>\n+ <param name="trailing_bp" type="integer" value="" min="0" optional="true" label="Stop codon filtering end position base pairs" \n+ help="Do not reject translation is stop_codons are within base pairs of the BED end position for negative strand"/>\n+ </when>\n+ <when value="no"/>\n+ </conditional>\n+ <conditional name="trim">\n+ <param name="trimseqs" type="select" label="Trim translations to stop codons">\n+ <option value="yes" selected="true">Yes</option>\n+ <option value="no">No</option>\n+ </param>\n+ <when value="no">\n+ <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"/>\n+ </when>\n+ </conditional>\n+ <param name="min_length" type="integer" value="" min="0" optional="true" label="Minimum length of a translation to be reported"/>\n+ </inputs>\n+ <outputs>\n+ <data name="translated_bed" metadata_source="input" format="bed" label="${tool.name} on ${on_string} bed" />\n+ <data name="output" metadata_source="input" format="fasta" label="${tool.name} on ${on_string} fasta" />\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="input" value="Extract_Genomic_DNA.bed" ftype="bed" dbkey="hg19"/>\n+ <param name="reference" value="GRCh37"/>\n+ <param name="seqtype" value="pep:novel"/>\n+ <param name="score_name" value="depth"/>\n+ <output name="output" file="translated_bed_sequences.fa"/>\n+ </test>\n+ </tests>\n+ <help>\n **Translate BED Sequences**\n \n This tool takes a BED input file that has been processed \n@@ -124,5 +121,5 @@\n It generates a peptide fasta file with the 3-frame translations of the spliced sequence \n defined by each entry in the input BED file.\n \n- </help>\n+ </help>\n </tool>\n' |