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changeset 1:ff53cf0d0bbd draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 8a69e869b86c4c371c18e7fde1e6b6af41f315a4"
author artbio
date Fri, 28 May 2021 23:32:25 +0000
parents b64b9a2bf4f0
children a5758bb680c8
files xpore_dataprep.xml xpore_diffmod.xml
diffstat 2 files changed, 23 insertions(+), 16 deletions(-) [+]
line wrap: on
line diff
--- a/xpore_dataprep.xml	Wed May 26 23:14:24 2021 +0000
+++ b/xpore_dataprep.xml	Fri May 28 23:32:25 2021 +0000
@@ -1,8 +1,7 @@
-<tool id="xpore_dataprep" name="xpore-dataprep" version="0.5.6+galaxy1">
+<tool id="xpore_dataprep" name="xpore-dataprep" version="0.5.6+galaxy2">
   <description></description>
   <requirements>
         <requirement type="package" version="0.5.6">xpore</requirement>
-        <requirement type="package" version="1.9.0">pyensembl</requirement>
   </requirements>
   <stdio>
       <exit_code range="1:" level="fatal" description="Tool exception" />
@@ -13,7 +12,14 @@
             --summary '$eventalign_summary'
             --out_dir out
             --n_processes \${GALAXY_SLOTS:-4} &&
-            ls -la out
+            mv ./out/data.index $data_index &&
+            mv ./out/eventalign.hdf5 $eventalign_hdf5 &&
+            mv ./out/data.log $data_log &&
+            mv ./out/eventalign.log $eventalign_log &&
+            mv ./out/data.readcount $data_readcount &&
+            mv ./out/data.json $data_json
+            
+            
   ]]></command>
  <inputs>
     <param name="eventalign_reads" type="data" format="txt,tabular" label="aligned nanopore events"
@@ -23,12 +29,12 @@
  </inputs>
 
  <outputs>
-    <data format="txt" name="data_index" label="data.index" from_work_dir="./out/data.index" />
-    <data format="h5" name="eventalign_hdf5" label="eventalign.hdf5" from_work_dir="./out/eventalign.hdf5" />
-    <data format="txt" name="data_log" label="data.log" from_work_dir="./out/data.log" />
-    <data format="txt" name="eventalign_log" label="eventalign.log" from_work_dir="./out/eventalign.log" />
-    <data format="txt" name="data_readcount" label="data.readcount" from_work_dir="./out/data.readcount" />
-    <data format="json" name="data_json" label="data.json" from_work_dir="./out/data.json"/>
+    <data format="txt" name="data_index" label="data.index" />
+    <data format="h5" name="eventalign_hdf5" label="eventalign.hdf5" />
+    <data format="txt" name="data_log" label="data.log" />
+    <data format="txt" name="eventalign_log" label="eventalign.log" />
+    <data format="txt" name="data_readcount" label="data.readcount" />
+    <data format="json" name="data_json" label="data.json" />
 </outputs>
 
 <tests>
--- a/xpore_diffmod.xml	Wed May 26 23:14:24 2021 +0000
+++ b/xpore_diffmod.xml	Fri May 28 23:32:25 2021 +0000
@@ -1,8 +1,7 @@
-<tool id="xpore_diffmod" name="xpore-diffmod" version="0.5.6+galaxy1">
+<tool id="xpore_diffmod" name="xpore-diffmod" version="0.5.6+galaxy2">
   <description></description>
   <requirements>
         <requirement type="package" version="0.5.6">xpore</requirement>
-        <requirement type="package" version="1.9.0">pyensembl</requirement>
   </requirements>
   <stdio>
       <exit_code range="1:" level="fatal" description="Tool exception" />
@@ -31,9 +30,11 @@
     printf "    prefiltering:\n" >> config.yml &&
     printf "        method: t-test\n" >> config.yml &&
     printf "        threshold: 0.1\n" >> config.yml &&
-
     xpore-diffmod --config config.yml  --n_processes \${GALAXY_SLOTS:-4} &&
-    sed -i "s/,/\t/g" ./out/diffmod.table
+    sed -i "s/,/\t/g" ./out/diffmod.table &&
+    mv ./out/diffmod.table $diffmod_table &&
+    mv ./out/diffmod.log $diffmod_log &&
+    mv ./config.yml $config
 
   ]]></command>
  <inputs>
@@ -64,9 +65,9 @@
  </inputs>
 
  <outputs>
-    <data format="tabular" name="diffmod_table" label="diffmod table" from_work_dir="./out/diffmod.table" />
-    <data format="txt" name="diffmod_log" label="diffmod log" from_work_dir="./out/diffmod.log" />
-    <data format="txt" name="config" label="configuration.yml" from_work_dir="./config.yml" />
+    <data format="tabular" name="diffmod_table" label="diffmod table" />
+    <data format="txt" name="diffmod_log" label="diffmod log" />
+    <data format="txt" name="config" label="configuration.yml" />
 </outputs>
 <tests>
     <test>