Mercurial > repos > peterjc > ncbi_blast_plus

changeset 42:fa7be13bcba9 draft

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Uploaded v0.1.0 preview 5, test extra column output
author peterjc
date Thu, 27 Feb 2014 06:41:09 -0500
parents af4da561893b
children d1330f50deb9
files test-data/four_human_proteins_taxid.fasta.pin tools/ncbi_blast_plus/README.rst tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
diffstat 3 files changed, 16 insertions(+), 1 deletions(-) [+]
line wrap: on
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Binary file test-data/four_human_proteins_taxid.fasta.pin has changed
--- a/tools/ncbi_blast_plus/README.rst	Wed Feb 26 13:26:14 2014 -0500
+++ b/tools/ncbi_blast_plus/README.rst	Thu Feb 27 06:41:09 2014 -0500
@@ -159,7 +159,7 @@
         - Now depends on package_blast_plus_2_2_28 in ToolShed.
         - Extended tabular output includes 'salltitles' as column 25.
 v0.1.00 - Now depends on package_blast_plus_2_2_29 in ToolShed.
-        - Tablar output now includes option to pick specific columns,
+        - Tabular output now includes option to pick specific columns,
           including previously unavailable taxonomy columns.
         - BLAST XML to tabular tool supports multiple input files.
         - More detailed descriptions for BLASTN and BLASTP task option.
--- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml	Wed Feb 26 13:26:14 2014 -0500
+++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml	Thu Feb 27 06:41:09 2014 -0500
@@ -83,6 +83,21 @@
             <param name="adv_opts_selector" value="basic" />
             <output name="output1" file="blastx_rhodopsin_vs_four_human_ext.tabular" ftype="tabular" />
         </test>
+        <test>
+            <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
+            <param name="db_opts_selector" value="file" />
+            <param name="subject" value="four_human_proteins.fasta" ftype="fasta" />
+            <param name="database" value="" />
+            <param name="evalue_cutoff" value="1e-10" />
+            <param name="out_format" value="cols" />
+            <param name="std_cols" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore" />
+            <param name="ext_cols" value="sallseqid,score,nident,positive,gaps,ppos,qframe,sframe,qseq,sseq,qlen,slen,salltitles" />
+            <param name="ids_cols" value="qgi,qacc,qaccver,sallseqid,sgi,sallgi,sacc,saccver,sallacc,stitle" />
+            <param name="misc_cols" value="sstrand,frames,btop,qcovs,qcovhsp" />
+            <param name="tax_cols" value="staxids,sscinames,scomnames,sblastnames,sskingdoms" />
+            <param name="adv_opts_selector" value="basic" />
+            <output name="output1" file="blastx_rhodopsin_vs_four_human_all.tabular" ftype="tabular" />
+        </test>
     </tests>
     <help>