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changeset 1:fbbe507e692b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 9028fa28c7b3216926bf999dd21c5f156d1cc63e
author iuc
date Sat, 04 Aug 2018 12:22:14 -0400
parents b2f1cf977ca9
children 6ad9d48a512e
files migmap.xml
diffstat 1 files changed, 5 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/migmap.xml	Sat Sep 30 09:33:24 2017 -0400
+++ b/migmap.xml	Sat Aug 04 12:22:14 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="migmap" name="MiGMAP" version="1.0.2.1">
+<tool id="migmap" name="MiGMAP" version="1.0.2.2">
     <description>mapper for full-length T- and B-cell repertoire sequencing
     </description>
     <requirements>
@@ -6,6 +6,9 @@
     </requirements>
     <command detect_errors='exit_code'><![CDATA[
 export IGBLAST_PATH=\$(dirname \$(which igblastn)) &&
+mkdir temp_db &&
+ln -s "\${IGBLAST_PATH}/../share/igblast/" ./temp_db/ &&
+
 #if $input.is_of_type('fasta') :
     ln -s '$input' in.fa &&
 #else
@@ -22,10 +25,9 @@
         -q $qual_threshold
     #end if
     -p "\${GALAXY_SLOTS:-4}"
-    --data-dir "\${IGBLAST_PATH}/../share/igblast"
+    --data-dir ./temp_db/igblast/
     -S $species 
     -R $receptor_list
-    --report '$report'
     #if $input.is_of_type('fasta'): 
         in.fa
     #else
@@ -71,7 +73,6 @@
     </inputs>
     <outputs>
         <data name="output" format="tabular"/>
-        <data name="report" format="txt"/>
     </outputs>
     <tests>
         <test>