diff macro.xml @ 0:d783eb846f59 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macro.xml	Sat Jan 13 09:02:58 2018 -0500
@@ -0,0 +1,77 @@
+<?xml version="1.0"?>
+<macros>
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="0.5.6">mykrobe</requirement>
+    </requirements>    
+  </xml>
+
+  <token name="@select_inputs@">
+    <![CDATA[
+         #set $name='sample'
+         #set $type='fastq'
+         ## Adding sample name, indicate specie and inputs fastq(s) files
+          #if $data_type.type == "paired":
+
+            ln -s '$data_type.fastq_input1' sample_1.fastq &&
+            ln -s '$data_type.fastq_input2' sample_2.fastq &&
+
+
+        #elif $data_type.type == "collection":
+            #set $name=str($data_type.fastq_input1.name)
+            ln -s '$data_type.fastq_input1.forward' '$data_type.fastq_input1.name'_1.fastq &&
+            ln -s '$data_type.fastq_input1.reverse' '$data_type.fastq_input1.name'_2.fastq &&
+
+        #elif $data_type.type == "single":
+
+
+            #if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'):
+              ln -s '$data_type.fastq_input1' sample.fastq &&
+
+            #end if
+
+            #if $data_type.fastq_input1.is_of_type('bam'):
+              ln -s '$data_type.fastq_input1' sample.bam &&
+              #set $type='bam'
+            #end if
+
+        #end if
+    ]]>
+  </token>
+
+  <xml name="inputs">
+    <conditional name="data_type">
+      <param name="type" type="select" label="Specify the read type.">
+        <option value="single">Single-end Data</option>
+        <option value="paired">Paired-end Data</option>
+        <option value="collection">Collection Paired-end Data</option>
+      </param>
+      <when value="single">
+        <param name="fastq_input1" type="data" format="fastqsanger, fastq,fasta,bam" label="Single end read file(s)"/>
+      </when>
+      <when value="paired">
+        <param name="fastq_input1" type="data" format="fastqsanger, fastq" label="Forward paired-end read file"/>
+        <param name="fastq_input2" type="data" format="fastqsanger, fastq" label="Reverse paired-end read file"/>
+      </when>
+      <when value="collection">
+        <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger, fastq" collection_type="paired" />
+      </when>
+    </conditional>
+  </xml>
+
+  <token name="@ATTRIBUTION@">
+    <![CDATA[
+             
+             **MyKrobe predict - Antibiotic resistance predictions**
+             
+             Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis
+             using Bruijn graph.
+    ]]>      
+  </token>
+
+  <xml name="citation">
+    <citations>
+      <citation type="doi">10.1038/ncomms10063</citation>
+    </citations>
+  </xml>
+</macros>