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changeset 19:7f3c448e119b draft

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v0.1.07 - fix macro problem in blastxml_to_tabular.xml, reenable .loc tests
author peterjc
date Thu, 19 Nov 2015 06:30:35 -0500
parents 577d9c12411a
children 3034ce97dd33
files tools/ncbi_blast_plus/README.rst tools/ncbi_blast_plus/blastxml_to_tabular.xml tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml tools/ncbi_blast_plus/ncbi_macros.xml tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml tools/ncbi_blast_plus/tool_dependencies.xml
diffstat 9 files changed, 9 insertions(+), 17 deletions(-) [+]
line wrap: on
line diff
--- a/tools/ncbi_blast_plus/README.rst	Mon Sep 07 04:44:24 2015 -0400
+++ b/tools/ncbi_blast_plus/README.rst	Thu Nov 19 06:30:35 2015 -0500
@@ -223,6 +223,10 @@
         - Update citation information now GigaScience paper is out.
 v0.1.06 - Now depends on ``package_blast_plus_2_2_31`` in ToolShed.
         - Tests updated for BLAST+ 2.2.31 instead of BLAST+ 2.2.30.
+v0.1.07 - Re-enabled some ``*.loc`` file tests (these had not been supported
+          on the Tool Shed test framework, but that is not currently in use).
+        - Fixed macro problem with version field in blastxml_to_tabular.xml
+          (contribution from Bjoern Gruening and Daniel Blankenberg).
 ======= ======================================================================
 
 
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml	Mon Sep 07 04:44:24 2015 -0400
+++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml	Thu Nov 19 06:30:35 2015 -0500
@@ -1,5 +1,8 @@
 <tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="@WRAPPER_VERSION@">
     <description>Convert BLAST XML output to tabular</description>
+    <macros>
+        <import>ncbi_macros.xml</import>
+    </macros>
     <stdio>
         <!-- Anything other than zero is an error -->
         <exit_code range="1:" />
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml	Mon Sep 07 04:44:24 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml	Thu Nov 19 06:30:35 2015 -0500
@@ -15,8 +15,6 @@
         <data name="info" format="txt" label="${db_opts.database.fields.name} info" />
     </outputs>
     <tests>
-        <!-- Disable for ToolShed where *.loc tests not yet supported
-             See https://github.com/peterjc/galaxy_blast/issues/53
         <test>
             <param name="db_opts|db_type" value="prot" />
             <param name="db_opts|database" value="four_human_proteins" />
@@ -27,7 +25,6 @@
             <param name="db_opts|database" value="three_human_mRNA" />
             <output name="info" file="three_human_mRNA.dbinfo.txt" ftype="txt" lines_diff="4" />
         </test>
-        -->
     </tests>
     <help>
     
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml	Mon Sep 07 04:44:24 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml	Thu Nov 19 06:30:35 2015 -0500
@@ -70,8 +70,6 @@
         <data name="seq" format="fasta" label="Sequences from ${db_opts.database.fields.name}" />
     </outputs>
     <tests>
-        <!-- Disable for ToolShed where *.loc tests not yet supported
-             See https://github.com/peterjc/galaxy_blast/issues/53
         <test>
             <param name="db_opts|db_type" value="prot" />
             <param name="db_opts|database" value="four_human_proteins" />
@@ -80,7 +78,6 @@
             <param name="outfmt" value="original" />
             <output name="seq" file="four_human_proteins.fasta" ftype="fasta" />
         </test>
-        -->
     </tests>
     <help>
     
--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Mon Sep 07 04:44:24 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Thu Nov 19 06:30:35 2015 -0500
@@ -102,8 +102,6 @@
             <param name="adv_opts_selector" value="basic" />
             <output name="output1" file="blastn_rhodopsin_vs_three_human.columns.tabular" ftype="tabular" />
         </test>
-        <!-- Disable for ToolShed where *.loc tests not yet supported
-             See https://github.com/peterjc/galaxy_blast/issues/53
         <test>
             <param name="query" value="chimera.fasta" ftype="fasta" />
             <param name="db_opts_selector" value="db" />
@@ -122,7 +120,6 @@
             <param name="max_hits" value="1" />
             <output name="output1" file="blastn_chimera_vs_three_human_max1.txt" ftype="txt" />
         </test>
-        -->
     </tests>
     <help>
     
--- a/tools/ncbi_blast_plus/ncbi_macros.xml	Mon Sep 07 04:44:24 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_macros.xml	Thu Nov 19 06:30:35 2015 -0500
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@WRAPPER_VERSION@">0.1.06</token>
+    <token name="@WRAPPER_VERSION@">0.1.07</token>
     <xml name="parallelism">
         <!-- If job splitting is enabled, break up the query file into parts -->
         <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1" />
--- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml	Mon Sep 07 04:44:24 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml	Thu Nov 19 06:30:35 2015 -0500
@@ -51,8 +51,6 @@
         </data>
     </outputs>
     <tests>
-        <!-- Disable for ToolShed where *.loc tests not yet supported
-             See https://github.com/peterjc/galaxy_blast/issues/53
         <test>
             <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
             <param name="db_opts_selector" value="db" />
@@ -61,7 +59,6 @@
             <param name="out_format" value="6" />
             <output name="output1" file="empty_file.dat" ftype="tabular" />
         </test>
-        -->
     </tests>
     <help>
     
--- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml	Mon Sep 07 04:44:24 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml	Thu Nov 19 06:30:35 2015 -0500
@@ -51,8 +51,6 @@
         </data>
     </outputs>
     <tests>
-        <!-- Disable for ToolShed where *.loc tests not yet supported
-             See https://github.com/peterjc/galaxy_blast/issues/53
         <test>
             <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
             <param name="db_opts_selector" value="db" />
@@ -61,7 +59,6 @@
             <param name="out_format" value="6" />
             <output name="output1" file="empty_file.dat" ftype="tabular" />
         </test>
-        -->
     </tests>
     <help>
     
--- a/tools/ncbi_blast_plus/tool_dependencies.xml	Mon Sep 07 04:44:24 2015 -0400
+++ b/tools/ncbi_blast_plus/tool_dependencies.xml	Thu Nov 19 06:30:35 2015 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="blast+" version="2.2.31">
-        <repository changeset_revision="e36f75574aec" name="package_blast_plus_2_2_31" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="16e1254ed634" name="package_blast_plus_2_2_31" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>