# HG changeset patch
# User estrain
# Date 1540124348 14400
# Node ID 454e2f1ccff42aac9b46a5f786c51c8fb27dd23d

Uploaded

diff -r 000000000000 -r 454e2f1ccff4 confindr.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/confindr.xml	Sun Oct 21 08:19:08 2018 -0400
@@ -0,0 +1,93 @@
+<tool id="confindr" name="confindr" label="Detect sequence contamination using rMLST" version="0.1.3">
+    <requirements>
+        <requirement type="package" version="0.4.3">confindr</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+      mkdir in out;
+      #if $jobtype.select == "fastq_single"
+        perl $__tool_directory__/makein.pl in $jobtype.fastq1 $jobtype.fastq1.name;
+      #else if $jobtype.select == "fastq_fr"
+        perl $__tool_directory__/makein.pl in $jobtype.fastq1 $jobtype.fastq1.name;
+        perl $__tool_directory__/makein.pl in $jobtype.fastq2 $jobtype.fastq2.name;
+      #else if $jobtype.select == "fastq_pair"
+        perl $__tool_directory__/makein.pl in $jobtype.coll.forward $jobtype.coll.forward.name;
+        perl $__tool_directory__/makein.pl in $jobtype.coll.reverse $jobtype.coll.reverse.name;
+      #end if
+      confindr.py -i in -o out
+      #if $options.select=="advanced"
+        #if $options.threads
+          -t $options.threads
+        #end if
+        #if $options.quality
+          -q $options.quality
+        #end if
+        #if $options.basecut
+          -b $options.basecut
+        #end if
+        #if $options.basefrac
+          -bf $options.basefrac
+        #end if
+        #if $options.datatype
+          -dt $options.datatype
+        #end if
+      #else if $options.select=="basic"
+        -t \${GALAXY_SLOTS:-1}
+      #end if
+    ]]></command>
+    <inputs>
+      <conditional name="jobtype">
+        <param name="select" type="select" label="Select Input">
+          <option value="fastq_single">Single FASTQ</option>
+          <option value="fastq_fr">Forward and Reverse FASTQ</option>
+          <option value="fastq_pair">Paired FASTQ Collection</option>
+        </param>
+        <when value="fastq_single">
+          <param name="fastq1" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="FASTQ" />
+        </when>
+        <when value="fastq_fr">
+          <param name="fastq1" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="Forward FASTQ" />
+          <param name="fastq2" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="Reverse FASTQ" />
+        </when>
+        <when value="fastq_pair">
+          <param name="coll" label="Paired FASTQ" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
+        </when>
+      </conditional>
+      <conditional name="options">
+        <param name="select" type="select" label="Basic or Advanced Settings">
+          <option value="basic">Basic</option>
+          <option value="advanced">Advanced</option>
+        </param>
+        <when value="advanced">
+          <param name="threads" optional="true" type="integer" label="Number of threads (Default=all)" value=""/>
+          <param name="quality" optional="true" type="integer" label="Base quality needed to support a multiple allele call (Default=20)" value=""/>
+          <param name="basecut" optional="true" type="integer" label="Number of bases necessary to support a multiple allele call (Default=2)" value=""/>
+          <param name="basefrac" optional="true" type="float" label="Fraction of bases necessary to support a multiple call." value="">
+            <validator type="in_range" message="Must be float(0,1)." min="0" max="1"/>
+          </param>
+	  <param name="datatype" type="select" label="Data Type">
+            <option value="Illumina">Illumina</option>
+            <option value="Nanopore">Nanopore</option>
+            <option value="auto">auto</option>
+          </param>
+        </when>
+        <when value="basic">
+        </when>
+      </conditional>
+    </inputs>
+    <outputs>
+      <data name="output" type="data" label="${tool.name} on ${on_string}" format="tabular" from_work_dir="out/confindr_report.csv" />
+    </outputs>
+    <help><![CDATA[
+    ]]></help>
+    <citations>
+      <citation type="bibtex">
+        @misc{githubconfindr,
+        author = {Low,Andrew},
+        year = {2018},
+        title = {confindr},
+        publisher = {GitHub},
+        journal = {GitHub repository},
+        url = {https://github.com/lowandrew/ConFindr},
+      }</citation>
+    </citations>
+</tool>