Mercurial > repos > iuc > transtermhp

changeset 3:1a1ec22a7e28 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 581d451609b919893ba53d104a5bcf2e9e565d1d
author iuc
date Wed, 07 Jun 2017 07:53:53 -0400
parents 1d8ad7599f02
children 9a90656a1af9
files all_fasta.loc.sample macros.xml tool_data_table_conf.xml.sample tool_dependencies.xml transtermhp.py transtermhp.xml
diffstat 6 files changed, 43 insertions(+), 50 deletions(-) [+]
line wrap: on
line diff
--- 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
@@ -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,
--- a/macros.xml	Fri Oct 09 09:40:48 2015 -0400
+++ b/macros.xml	Wed Jun 07 07:53:53 2017 -0400
@@ -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>
--- 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
@@ -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>
--- a/tool_dependencies.xml	Fri Oct 09 09:40:48 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -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>
--- a/transtermhp.py	Fri Oct 09 09:40:48 2015 -0400
+++ b/transtermhp.py	Wed Jun 07 07:53:53 2017 -0400
@@ -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)
--- a/transtermhp.xml	Fri Oct 09 09:40:48 2015 -0400
+++ b/transtermhp.xml	Wed Jun 07 07:53:53 2017 -0400
@@ -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.