| Previous changeset 2:1d8ad7599f02 (2015-10-09) Next changeset 4:9a90656a1af9 (2018-10-30) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 581d451609b919893ba53d104a5bcf2e9e565d1d |
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modified:
all_fasta.loc.sample macros.xml tool_data_table_conf.xml.sample transtermhp.py transtermhp.xml |
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removed:
tool_dependencies.xml |
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| diff -r 1d8ad7599f02 -r 1a1ec22a7e28 all_fasta.loc.sample --- a/all_fasta.loc.sample Fri Oct 09 09:40:48 2015 -0400 +++ b/all_fasta.loc.sample Wed Jun 07 07:53:53 2017 -0400 |
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| @@ -4,13 +4,13 @@ #all_fasta.loc. This file has the format (white space characters are #TAB characters): # -#<unique_build_id> <dbkey> <display_name> <file_path> +#<unique_build_id> <dbkey> <display_name> <file_path> # #So, all_fasta.loc could look something like this: # -#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa -#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa -#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa # #Your all_fasta.loc file should contain an entry for each individual #fasta file. So there will be multiple fasta files for each build, |
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| diff -r 1d8ad7599f02 -r 1a1ec22a7e28 macros.xml --- a/macros.xml Fri Oct 09 09:40:48 2015 -0400 +++ b/macros.xml Wed Jun 07 07:53:53 2017 -0400 |
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| @@ -3,8 +3,9 @@ <xml name="requirements"> <requirements> <requirement type="package" version="2.09">transtermhp</requirement> - <requirement type="package" version="1.65">biopython</requirement> - <requirement type="package" version="0.6.2">bcbiogff</requirement> + <requirement type="package" version="1.69">biopython</requirement> + <requirement type="package" version="0.6.4">bcbiogff</requirement> + <requirement type="package" version="2.7">python</requirement> <yield/> </requirements> </xml> |
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| diff -r 1d8ad7599f02 -r 1a1ec22a7e28 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Fri Oct 09 09:40:48 2015 -0400 +++ b/tool_data_table_conf.xml.sample Wed Jun 07 07:53:53 2017 -0400 |
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| @@ -1,7 +1,7 @@ <!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> <tables> <!-- Locations of all fasta files under genome directory --> - <table name="all_fasta" comment_char="#"> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> <columns>value, dbkey, name, path</columns> <file path="tool-data/all_fasta.loc" /> </table> |
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| diff -r 1d8ad7599f02 -r 1a1ec22a7e28 tool_dependencies.xml --- a/tool_dependencies.xml Fri Oct 09 09:40:48 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,12 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="transtermhp" version="2.09"> - <repository changeset_revision="0a21f73e2f15" name="package_transtermhp_2_09" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="biopython" version="1.65"> - <repository changeset_revision="dc595937617c" name="package_biopython_1_65" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="bcbiogff" version="0.6.2"> - <repository changeset_revision="8adfe232049d" name="package_python_2_7_bcbiogff_0_6_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |
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| diff -r 1d8ad7599f02 -r 1a1ec22a7e28 transtermhp.py --- a/transtermhp.py Fri Oct 09 09:40:48 2015 -0400 +++ b/transtermhp.py Wed Jun 07 07:53:53 2017 -0400 |
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| @@ -1,10 +1,14 @@ #!/usr/bin/env python -import sys import re import subprocess -from Bio import SeqIO +import sys + from BCBio import GFF -from Bio.SeqFeature import SeqFeature, FeatureLocation +from Bio import SeqIO +from Bio.SeqFeature import ( + FeatureLocation, + SeqFeature +) def main(expterm, fasta, gff3): @@ -65,6 +69,7 @@ rec.features.append(feature) yield rec + if __name__ == '__main__': for record in main(*sys.argv[1:4]): GFF.write([record], sys.stdout) |
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| diff -r 1d8ad7599f02 -r 1a1ec22a7e28 transtermhp.xml --- a/transtermhp.xml Fri Oct 09 09:40:48 2015 -0400 +++ b/transtermhp.xml Wed Jun 07 07:53:53 2017 -0400 |
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| @@ -1,27 +1,26 @@ -<?xml version="1.0"?> -<tool id="transtermhp" name="TransTermHP" version="@WRAPPER_VERSION@.0"> - <description>finds rho-independent transcription terminators in bacterial genomes</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"/> - <expand macro="stdio"/> - <command><![CDATA[ +<tool id="transtermhp" name="TransTermHP" version="@WRAPPER_VERSION@.1"> + <description>finds rho-independent transcription terminators in bacterial genomes</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <command><![CDATA[ #if $reference_genome.source == 'history': - ln -s $reference_genome.genome_fasta genomeref.fa && + ln -s '$reference_genome.genome_fasta' genomeref.fa && #end if -python $__tool_directory__/transtermhp.py \$TRANSTERM_EXPTERM_DAT +python '$__tool_directory__/transtermhp.py' \$TRANSTERMHP #if $reference_genome.source == 'cached': - "${reference_genome.fasta_indexes.fields.path}" + '${reference_genome.fasta_indexes.fields.path}' #elif $reference_genome.source == 'history': genomeref.fa #end if -$input_gff3 - -> $output]]></command> +'$input_gff3' +> '$output' + ]]></command> <inputs> <conditional name="reference_genome"> <param name="source" type="select" label="Reference Genome"> @@ -54,19 +53,19 @@ This is a TODO item that would be nice to get around to eventually (perhaps when a user demands it.) --> - </inputs> - <outputs> - <data format="gff3" name="output"/> - </outputs> - <tests> - <test> - <param name="source" value="history" /> - <param name="genome_fasta" value="sequence.fasta" /> - <param name="input_gff3" value="sequence.gff3" /> - <output name="output" file="sequence.gff3.out" /> - </test> - </tests> - <help><![CDATA[ + </inputs> + <outputs> + <data format="gff3" name="output"/> + </outputs> + <tests> + <test> + <param name="source" value="history" /> + <param name="genome_fasta" value="sequence.fasta" /> + <param name="input_gff3" value="sequence.gff3" /> + <output name="output" file="sequence.gff3.out" /> + </test> + </tests> + <help><![CDATA[ **What it does** Finds rho-independent transcription terminators in bacterial genomes. |