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changeset 12:8f70b0652cff draft

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planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/mash commit 423cf96266f6ac433052ff72edb1397502313010-dirty
author dfornika
date Thu, 25 Jul 2019 17:32:55 -0400
parents d85f64b694ca
children 41c3042e0d54
files fasta_from_mash_sketch_data_table.xml mash_screen.xml
diffstat 2 files changed, 27 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fasta_from_mash_sketch_data_table.xml	Thu Jul 25 17:32:55 2019 -0400
@@ -0,0 +1,26 @@
+<tool id="fasta_from_mash_sketch_data_table" name="get fasta from mash_sketches data table" version="@TOOL_VERSION@+galaxy0">
+    <description>Extracts fasta file from mash_sketches data table.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        cp '${queries.fields.path}/seqs.fasta' '$output'
+    ]]></command>
+    <inputs>
+	<param name="queries" type="select">
+            <options from_data_table="mash_sketches">
+                <validator type="no_options" message="No mash sketches are available." />
+            </options>
+        </param>
+    <outputs>
+        <data name="output" format="fasta" />
+    </outputs>
+    <tests>
+    </tests>
+    <help><![CDATA[
+    ]]></help>
+    <citations>
+    </citations>
+</tool>
--- a/mash_screen.xml	Thu Jul 25 15:50:37 2019 -0400
+++ b/mash_screen.xml	Thu Jul 25 17:32:55 2019 -0400
@@ -10,7 +10,7 @@
     <command detect_errors="exit_code"><![CDATA[
         ln -s '${queries.fields.path}/sketch.msh' queries.msh &&
         mash screen
-             -p \${GALAXY_SLOTS:-4}  
+             -p \${GALAXY_SLOTS:-1}  
              $winner_takes_all
              -i $minimum_identity_to_report
              -v $maximum_p_value_to_report