# HG changeset patch
# User dfornika
# Date 1569009582 14400
# Node ID ddae1e5b4bb24a6e2d2c938215cba8c18a1dc2fd
# Parent  ce0afe2b18d0b4033e1ba330e2224b27850f00f0
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/micall-lite commit c8241b460c9def5b434fa4350924599b09b17a69-dirty

diff -r ce0afe2b18d0 -r ddae1e5b4bb2 micall-lite.xml
--- a/micall-lite.xml	Thu Sep 19 19:57:29 2019 -0400
+++ b/micall-lite.xml	Fri Sep 20 15:59:42 2019 -0400
@@ -7,36 +7,20 @@
         <requirement type="package" version="@TOOL_VERSION@">micall-lite</requirement>
     </requirements>
     <version_command>micall --version</version_command>
-    <command detect_errors="exit_code"><![CDATA[
-      micall
-        #if $single_paired.single_paired_selector == 'yes'
-            '${single_paired.forward_input}' '${single_paired.reverse_input}'
-        #elif $single_paired.single_paired_selector == "collection":
-            '${single_paired.input_pair.forward}' '${single_paired.input_pair.reverse}'
-        #else:
-            '${single_paired.input_sequences}'
-        #end if
-    ]]></command>
+    <command detect_errors="exit_code">
+        <![CDATA[
+          ln -s '${input_pair.forward}' '${input_pair.element_identifier}_R1.fastq.gz' &&
+          ln -s '${input_pair.reverse}' '${input_pair.element_identifier}_R2.fastq.gz' &&
+          micall
+            '${input_pair.element_identifier}_R1.fastq.gz'
+            '${input_pair.element_identifier}_R2.fastq.gz'
+        ]]>
+    </command>
     <inputs>
-        <conditional name="single_paired">
-            <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
-                <option value="collection">Collection</option>
-                <option value="yes">Paired</option>
-                <option selected="True" value="no">Single</option>
-            </param>
-            <when value="collection">
-                <param format="fastq,fastq.gz" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTQ datasets" />
-            </when>
-            <when value="yes">
-                <param format="fastq,fastq.gz" name="forward_input" type="data" label="Forward strand" help="FASTQ dataset"/>
-                <param format="fastq,fastq.gz" name="reverse_input" type="data" label="Reverse strand" help="FASTQ dataset"/>
-            </when>
-            <when value="no">
-                <param format="fastq,fastq.gz" label="Input sequences" name="input_sequences" type="data" help="FASTQ datasets"/>
-            </when>
-        </conditional>
+        <param format="fastq,fastq.gz" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTQ datasets" />
     </inputs>
     <outputs>
+        <data name="conseq" format="tabular" ext="conseq.csv" />
     </outputs>
     <tests>
         <test>