Mercurial > repos > peterjc > ncbi_blast_plus

changeset 8:e710b9446493 draft

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Uploaded v0.0.19 preview 5, nicer output labels on datasets
author peterjc
date Thu, 25 Apr 2013 09:27:16 -0400
parents 08be1b2b0bf6
children b2eb4f48122f
files tools/ncbi_blast_plus/ncbi_blast_plus.txt 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_rpstblastn_wrapper.xml tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
diffstat 9 files changed, 11 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/tools/ncbi_blast_plus/ncbi_blast_plus.txt	Thu Apr 25 09:05:13 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blast_plus.txt	Thu Apr 25 09:27:16 2013 -0400
@@ -94,9 +94,10 @@
 v0.0.18 - Defensive quoting of filenames in case of spaces (where possible,
           BLAST+ handling of some mult-file arguments is problematic).
 v0.0.19 - Added wrappers for rpsblast and rpstblastn, and new blastdb_d.loc
-          for the domain databases they use (e.g. CDD).
+          for the domain databases they use (e.g. CDD, PFAM or SMART).
         - Correct case of exception regular expression (for error handling
           fall-back in case the return code is not set properly).
+        - Clearer naming of output files.
 
 
 Developers
--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Thu Apr 25 09:05:13 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Thu Apr 25 09:27:16 2013 -0400
@@ -136,7 +136,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="output1" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector}">
+        <data name="output1" format="tabular" label="${blast_type.value_label} on ${on_string}">
             <change_format>
                 <when input="out_format" value="0" format="txt"/>
                 <when input="out_format" value="0 -html" format="html"/>
--- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml	Thu Apr 25 09:05:13 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml	Thu Apr 25 09:27:16 2013 -0400
@@ -141,7 +141,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="output1" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector}">
+        <data name="output1" format="tabular" label="${blast_type.value_label} on ${on_string}">
             <change_format>
                 <when input="out_format" value="0" format="txt"/>
                 <when input="out_format" value="0 -html" format="html"/>
--- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml	Thu Apr 25 09:05:13 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml	Thu Apr 25 09:27:16 2013 -0400
@@ -158,7 +158,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="output1" format="tabular" label="blastx on ${db_opts.db_opts_selector}">
+        <data name="output1" format="tabular" label="blastx on ${on_string}">
             <change_format>
                 <when input="out_format" value="0" format="txt"/>
                 <when input="out_format" value="0 -html" format="html"/>
--- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml	Thu Apr 25 09:05:13 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml	Thu Apr 25 09:27:16 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.0.3">
+<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.0.4">
   <description>Make BLAST database</description>
     <requirements>
         <requirement type="binary">makeblastdb</requirement>
@@ -95,7 +95,7 @@
 </inputs>
 <outputs>
     <!-- If we only accepted one FASTA file, we could use its human name here... -->
-    <data name="outfile" format="data" label="BLAST database from ${on_string}">
+    <data name="outfile" format="data" label="${dbtype.value_label} BLAST database from ${on_string}">
         <change_format>
                 <when input="dbtype" value="nucl" format="blastdbn"/>
                 <when input="dbtype" value="prot" format="blastdbp"/>
--- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml	Thu Apr 25 09:05:13 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml	Thu Apr 25 09:27:16 2013 -0400
@@ -113,7 +113,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="output1" format="tabular" label="RPS-BLAST on ${db_opts.db_opts_selector}">
+        <data name="output1" format="tabular" label="rpsblast on ${on_string}">
             <change_format>
                 <when input="out_format" value="0" format="txt"/>
                 <when input="out_format" value="0 -html" format="html"/>
--- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml	Thu Apr 25 09:05:13 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml	Thu Apr 25 09:27:16 2013 -0400
@@ -114,7 +114,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="output1" format="tabular" label="RPS-TBLASTN on ${db_opts.db_opts_selector}">
+        <data name="output1" format="tabular" label="rpstblastn on ${on_string}">
             <change_format>
                 <when input="out_format" value="0" format="txt"/>
                 <when input="out_format" value="0 -html" format="html"/>
--- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml	Thu Apr 25 09:05:13 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml	Thu Apr 25 09:27:16 2013 -0400
@@ -158,7 +158,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="output1" format="tabular" label="tblastn on ${db_opts.db_opts_selector}">
+        <data name="output1" format="tabular" label="tblastn on ${on_string}">
             <change_format>
                 <when input="out_format" value="0" format="txt"/>
                 <when input="out_format" value="0 -html" format="html"/>
--- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml	Thu Apr 25 09:05:13 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml	Thu Apr 25 09:27:16 2013 -0400
@@ -178,7 +178,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="output1" format="tabular" label="tblastx on ${db_opts.db_opts_selector}">
+        <data name="output1" format="tabular" label="tblastx on ${on_string}">
             <change_format>
                 <when input="out_format" value="0" format="txt"/>
                 <when input="out_format" value="0 -html" format="html"/>