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changeset 5:d42346e675c4 draft

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Uploaded v0.0.19 pre-release attempt 2 This defines a package requirement in each wrapper.
author peterjc
date Wed, 17 Apr 2013 10:04:28 -0400
parents 4afb12181d1a
children e77e30f1deeb
files 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_blastp_wrapper.xml tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml tools/ncbi_blast_plus/ncbi_makeblastdb.xml tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
diffstat 9 files changed, 44 insertions(+), 29 deletions(-) [+]
line wrap: on
line diff
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml	Wed Apr 17 09:47:27 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml	Wed Apr 17 10:04:28 2013 -0400
@@ -1,5 +1,10 @@
-<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.0.4">
+<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.0.5">
     <description>Show BLAST database information from blastdbcmd</description>
+    <requirements>
+        <requirement type="binary">blastdbcmd</requirement>
+        <requirement type="package" version="2.2.26+">blast+</requirement>
+    </requirements>
+    <version_command>blastdbcmd -version</version_command>
     <command>
 blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}" -info -out "$info"
     </command>
@@ -40,9 +45,6 @@
     <outputs>
         <data name="info" format="txt" label="${db_opts.database.fields.name} info" />
     </outputs>
-    <requirements>
-        <requirement type="binary">blastdbcmd</requirement>
-    </requirements>
     <help>
     
 **What it does**
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml	Wed Apr 17 09:47:27 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml	Wed Apr 17 10:04:28 2013 -0400
@@ -1,5 +1,10 @@
-<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="0.0.4">
+<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="0.0.5">
     <description>Extract sequence(s) from BLAST database</description>
+    <requirements>
+        <requirement type="binary">blastdbcmd</requirement>
+        <requirement type="package" version="2.2.26+">blast+</requirement>
+    </requirements>
+    <version_command>blastdbcmd -version</version_command>
     <command>
 ## The command is a Cheetah template which allows some Python based syntax.
 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
@@ -95,9 +100,6 @@
     <outputs>
         <data name="seq" format="fasta" label="Sequences from ${db_opts.database.fields.name}" />
     </outputs>
-    <requirements>
-        <requirement type="binary">blastdbcmd</requirement>
-    </requirements>
     <help>
     
 **What it does**
--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Wed Apr 17 09:47:27 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Wed Apr 17 10:04:28 2013 -0400
@@ -2,6 +2,10 @@
     <description>Search nucleotide database with nucleotide query sequence(s)</description>
     <!-- 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" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism>
+    <requirements>
+        <requirement type="binary">blastn</requirement>
+        <requirement type="package" version="2.2.26+">blast+</requirement>
+    </requirements>
     <version_command>blastn -version</version_command>
     <command>
 ## The command is a Cheetah template which allows some Python based syntax.
@@ -144,9 +148,6 @@
             </change_format>
         </data>
     </outputs>
-    <requirements>
-        <requirement type="binary">blastn</requirement>
-    </requirements>
     <help>
     
 .. class:: warningmark
--- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml	Wed Apr 17 09:47:27 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml	Wed Apr 17 10:04:28 2013 -0400
@@ -2,6 +2,10 @@
     <description>Search protein database with protein query sequence(s)</description>
     <!-- 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" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism>
+    <requirements>
+        <requirement type="binary">blastp</requirement>
+        <requirement type="package" version="2.2.26+">blast+</requirement>
+    </requirements>
     <version_command>blastp -version</version_command>
     <command>
 ## The command is a Cheetah template which allows some Python based syntax.
@@ -149,9 +153,6 @@
             </change_format>
         </data>
     </outputs>
-    <requirements>
-        <requirement type="binary">blastp</requirement>
-    </requirements>
     <tests>
         <test>
             <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
--- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml	Wed Apr 17 09:47:27 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml	Wed Apr 17 10:04:28 2013 -0400
@@ -2,6 +2,10 @@
     <description>Search protein database with translated nucleotide query sequence(s)</description>
     <!-- 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" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism>
+    <requirements>
+        <requirement type="binary">blastx</requirement>
+        <requirement type="package" version="2.2.26+">blast+</requirement>
+    </requirements>
     <version_command>blastx -version</version_command>
     <command>
 ## The command is a Cheetah template which allows some Python based syntax.
@@ -166,9 +170,6 @@
             </change_format>
         </data>
     </outputs>
-    <requirements>
-        <requirement type="binary">blastx</requirement>
-    </requirements>
     <tests>
         <test>
             <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
--- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml	Wed Apr 17 09:47:27 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml	Wed Apr 17 10:04:28 2013 -0400
@@ -1,7 +1,11 @@
 <tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.0.3">
-<description>Make BLAST database</description>
-<version_command>makeblastdb -version</version_command>
-<command>
+  <description>Make BLAST database</description>
+    <requirements>
+        <requirement type="binary">makeblastdb</requirement>
+        <requirement type="package" version="2.2.26+">blast+</requirement>
+    </requirements>
+    <version_command>makeblastdb -version</version_command>
+    <command>
 makeblastdb -out "${os.path.join($outfile.extra_files_path,'blastdb')}"
 $parse_seqids
 $hash_index
@@ -100,6 +104,7 @@
 </outputs>
 <requirements>
     <requirement type="binary">makeblastdb</requirement>
+    <requirement type="package" version="2.2.26+">blast+</requirement>
 </requirements>
 <help>
 **What it does**
--- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml	Wed Apr 17 09:47:27 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml	Wed Apr 17 10:04:28 2013 -0400
@@ -2,6 +2,10 @@
     <description>Search protein domain database (PSSMs) with protein query sequence(s)</description>
     <!-- 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" shared_inputs="subject" merge_outputs="output1"></parallelism>
+    <requirements>
+        <requirement type="binary">rpsblast</requirement>
+        <requirement type="package" version="2.2.26+">blast+</requirement>
+    </requirements>
     <version_command>rpsblast -version</version_command>
     <command>
 ## The command is a Cheetah template which allows some Python based syntax.
@@ -121,9 +125,6 @@
             </change_format>
         </data>
     </outputs>
-    <requirements>
-        <requirement type="binary">rpsblast</requirement>
-    </requirements>
     <help>
     
 .. class:: warningmark
--- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml	Wed Apr 17 09:47:27 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml	Wed Apr 17 10:04:28 2013 -0400
@@ -2,6 +2,10 @@
     <description>Search translated nucleotide database with protein query sequence(s)</description>
     <!-- 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" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism>
+    <requirements>
+        <requirement type="binary">tblastn</requirement>
+        <requirement type="package" version="2.2.26+">blast+</requirement>
+    </requirements>
     <version_command>tblastn -version</version_command>
     <command>
 ## The command is a Cheetah template which allows some Python based syntax.
@@ -166,9 +170,6 @@
             </change_format>
         </data>
     </outputs>
-    <requirements>
-        <requirement type="binary">tblastn</requirement>
-    </requirements>
     <tests>
         <test>
             <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
--- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml	Wed Apr 17 09:47:27 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml	Wed Apr 17 10:04:28 2013 -0400
@@ -2,6 +2,10 @@
     <description>Search translated nucleotide database with translated nucleotide query sequence(s)</description>
     <!-- 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" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism>
+    <requirements>
+        <requirement type="binary">tblastx</requirement>
+        <requirement type="package" version="2.2.26+">blast+</requirement>
+    </requirements>
     <version_command>tblastx -version</version_command>
     <command>
 ## The command is a Cheetah template which allows some Python based syntax.
@@ -186,9 +190,6 @@
             </change_format>
         </data>
     </outputs>
-    <requirements>
-        <requirement type="binary">tblastx</requirement>
-    </requirements>
     <help>
     
 .. class:: warningmark