Mercurial > repos > jjohnson > defuse

changeset 16:bdd93719cede draft

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Uploaded
author jjohnson
date Mon, 18 Dec 2017 09:31:31 -0500
parents b67c24d902aa
children c3167ccca38c
files create_reference_dataset.xml datamanager_create_reference.xml defuse.xml defuse_bamfastq.xml defuse_results_to_vcf.xml defuse_trinity_analysis.xml macros.xml tool_dependencies.xml
diffstat 8 files changed, 19 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/create_reference_dataset.xml	Tue Dec 12 12:00:24 2017 -0500
+++ b/create_reference_dataset.xml	Mon Dec 18 09:31:31 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="create_defuse_reference" name="Create DeFuse Reference" version="@DEFUSE_VERSION@.1">
+<tool id="create_defuse_reference" name="Create DeFuse Reference" version="@DEFUSE_VERSION@.2">
  <description>create a defuse reference from Ensembl and UCSC sources</description>
     <macros>
         <import>macros.xml</import>
--- a/datamanager_create_reference.xml	Tue Dec 12 12:00:24 2017 -0500
+++ b/datamanager_create_reference.xml	Mon Dec 18 09:31:31 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="data_manager_defuse_reference" name="DeFuse Reference DataManager" version="1.6.1" tool_type="manage_data">
+<tool id="data_manager_defuse_reference" name="DeFuse Reference DataManager" version="@DEFUSE_VERSION@.2" tool_type="manage_data">
  <description>create a defuse reference from Ensembl and UCSC sources</description>
     <macros>
         <import>macros.xml</import>
@@ -112,11 +112,11 @@
     <when value="user_specified">
       <param name="ensembl_organism" type="text" value="" label="Ensembl Organism Name" help="Examples: homo_sapiens, mus_musculus, rattus_norvegicus"/>
       <param name="ensembl_prefix" type="text" value="" label="Ensembl Organism prefix" help="Examples: Homo_sapiens, Mus_musculus, Rattus_norvegicus"/>
-      <param name="ensembl_genome_version" type="text" value="" label="Ensembl Genome Version" help="Examples: GRCh37, GRCm38, Rnor_5.0"/>
-      <param name="ensembl_version" type="integer" value="" label="Ensembl Release Version" help="Example: 71"/>
+      <param name="ensembl_genome_version" type="text" value="" label="Ensembl Genome Version" help="Examples: GRCh38, GRCh37, GRCm38, Rnor_5.0"/>
+      <param name="ensembl_version" type="integer" value="" label="Ensembl Release Version" help="Example: 86"/>
       <param name="ncbi_organism" type="text" value="" label="NCBI Organism Name" help="Examples: Homo_sapiens, Mus_musculus, Rattus_norvegicus"/>
       <param name="ncbi_prefix" type="text" value="" label="NCBI Organism Unigene prefix" help="Examples: Hs, Mm, Rn"/>
-      <param name="ucsc_genome_version" type="text" value="" label="UCSC Genome Version" help="Examples: hg19, mm10, rn5"/>
+      <param name="ucsc_genome_version" type="text" value="" label="UCSC Genome Version" help="Examples: hg38, hg19, mm10, rn5"/>
       <param name="chromosomes" type="text" value="" label="Chromosomes for Ensembl genome build" >
        <help>  Examples: 
          Homo_sapiens: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT
--- a/defuse.xml	Tue Dec 12 12:00:24 2017 -0500
+++ b/defuse.xml	Mon Dec 18 09:31:31 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="defuse" name="DeFuse" version="@DEFUSE_VERSION@.1">
+<tool id="defuse" name="DeFuse" version="@DEFUSE_VERSION@.2">
     <description>identify fusion transcripts</description>
     <macros>
         <import>macros.xml</import>
--- a/defuse_bamfastq.xml	Tue Dec 12 12:00:24 2017 -0500
+++ b/defuse_bamfastq.xml	Mon Dec 18 09:31:31 2017 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="defuse_bamfastq" name="Defuse BamFastq" version="@DEFUSE_VERSION@.1">
+<tool id="defuse_bamfastq" name="Defuse BamFastq" version="@DEFUSE_VERSION@.2">
   <description>converts a bam file to fastq files.</description>
     <macros>
         <import>macros.xml</import>
--- a/defuse_results_to_vcf.xml	Tue Dec 12 12:00:24 2017 -0500
+++ b/defuse_results_to_vcf.xml	Mon Dec 18 09:31:31 2017 -0500
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
-<tool id="defuse_results_to_vcf" name="Defuse Results to VCF" version="0.6.1">
+<tool id="defuse_results_to_vcf" name="Defuse Results to VCF" version="@DEFUSE_VERSION@.2">
   <description>generate a VCF from a DeFuse Results file</description>
-  <requirements>
-    <requirement type="package" version="0.6.1">defuse</requirement>
-  </requirements>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
   <command interpreter="python">defuse_results_to_vcf.py  --input $defuse_results --reference ${defuse_results.metadata.dbkey} --output $vcf
   </command>
   <inputs>
--- a/defuse_trinity_analysis.xml	Tue Dec 12 12:00:24 2017 -0500
+++ b/defuse_trinity_analysis.xml	Mon Dec 18 09:31:31 2017 -0500
@@ -1,6 +1,9 @@
 <?xml version="1.0"?>
-<tool id="defuse_trinity_analysis" name="Defuse Trinity" version="0.6.1">
+<tool id="defuse_trinity_analysis" name="Defuse Trinity" version="@DEFUSE_VERSION@.2">
   <description>verify fusions with trinity</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
   <stdio>
     <exit_code range="1:" level="fatal" description="Error" />
   </stdio>
--- a/macros.xml	Tue Dec 12 12:00:24 2017 -0500
+++ b/macros.xml	Mon Dec 18 09:31:31 2017 -0500
@@ -8,6 +8,7 @@
             <requirement type="package" version="1.0.0">bowtie</requirement>
             <requirement type="package" version="2013-05-09">gmap</requirement>
             <requirement type="package" version="35x1">blat</requirement>
+            <requirement type="package" version="35x1">faToTwoBit</requirement>
     </xml>
     <xml name="r_requirements">
             <requirement type="package" version="3.1.2">R</requirement>
--- a/tool_dependencies.xml	Tue Dec 12 12:00:24 2017 -0500
+++ b/tool_dependencies.xml	Mon Dec 18 09:31:31 2017 -0500
@@ -15,6 +15,9 @@
     <package name="blat" version="35x1">
         <repository changeset_revision="cc0f4b49b6f1" name="package_blat_35x1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
+    <package name="faToTwoBit" version="35x1">
+        <repository changeset_revision="46615329ea72" name="package_fatotwobit_35x1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
     <package name="R" version="3.1.2">
         <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>