Mercurial > repos > stephenshank > hyphy_gard

changeset 2:5501955d58e1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
author stephenshank
date Tue, 06 Nov 2018 10:54:04 -0500
parents 0ea9da9cd6ad
children 0caaff912a55
files hyphy_gard.xml
diffstat 1 files changed, 3 insertions(+), 18 deletions(-) [+]
line wrap: on
line diff
--- a/hyphy_gard.xml	Tue Oct 30 10:56:18 2018 -0400
+++ b/hyphy_gard.xml	Tue Nov 06 10:54:04 2018 -0500
@@ -14,32 +14,17 @@
     ln -s '$input_file' gard_input.fa &&
     echo `pwd`/gard_input.fa > tool_params &&
     echo "010010" >> tool_params &&
-    echo $gencodeid >> tool_params &&
     echo $rate_cond.rate >> tool_params &&
     #if str($rate_cond.rate) != "1":
         echo $rate_cond.rate_classes >> tool_params &&
     #end if
-    echo `pwd`/"gard_input.fa.GARD.json" >> tool_params &&
+    echo `pwd`/"gard_input.GARD" >> tool_params &&
     @HYPHYMPI_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/GARD.bf > '$gard_log' &&
-    translate-gard -i gard_input.fa -j gard_input.fa.GARD.json -o gard_input.fa.translated.json
+    translate-gard -i `pwd`/gard_input.GARD -j `pwd`/gard_input.GARD.json -o gard_input.fa.translated.json
     ]]>
     </command>
     <inputs>
         <param name="input_file" type="data" format="fasta" label="Input FASTA file" />
-        <param name="gencodeid" type="select" label="Genetic code">
-            <option value="1">Universal code</option>
-            <option value="2">Vertebrate mitochondrial DNA code</option>
-            <option value="3">Yeast mitochondrial DNA code</option>
-            <option value="4">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option>
-            <option value="5">Invertebrate mitochondrial DNA code</option>
-            <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear code</option>
-            <option value="7">Echinoderm mitochondrial DNA code</option>
-            <option value="8">Euplotid Nuclear code</option>
-            <option value="9">Alternative Yeast Nuclear code</option>
-            <option value="10">Ascidian mitochondrial DNA code</option>
-            <option value="11">Flatworm mitochondrial DNA code</option>
-            <option value="12">Blepharisma Nuclear code</option>
-        </param>
         <conditional name="rate_cond">
             <param name="rate" type="select" label="Rate variation">
                 <option value="1">None</option>
@@ -57,7 +42,7 @@
     </inputs>
     <outputs>
         <data name="gard_log" format="txt" />
-        <data name="gard_output" format="json" from_work_dir="gard_input.fa.GARD.json" />
+        <data name="gard_output" format="nex" from_work_dir="gard_input.GARD_finalout" />
         <data name="translated" format="json" from_work_dir="gard_input.fa.translated.json" />
     </outputs>
     <tests>