# HG changeset patch
# User thanhlv
# Date 1591106829 14400
# Node ID 685f2f21f160d99970cc795329753266f766e799

Uploaded

diff -r 000000000000 -r 685f2f21f160 galru.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galru.xml	Tue Jun 02 10:07:09 2020 -0400
@@ -0,0 +1,70 @@
+<tool id="galru" name="galru" version="@VERSION@">
+    <description>Long read spoligotyping for Mycobacterium tuberculosis</description>
+    <macros>
+        <token name="@VERSION@">1.0.0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@VERSION@">galru</requirement>
+    </requirements>
+    <version_command>galru --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        galru
+        --technology $technology
+        #if str($cas_input.cas_select) == "history":
+            --cas_fasta '$cas_input.cas_file'
+        #end if
+        --gene_start_offset $gene_start_offset
+        --min_mapping_quality $min_mapping_quality
+        --qcov_margin $qcov_margin
+        --min_bitscore $min_bitscore
+        --min_identity $min_identity
+        --threads \${GALAXY_SLOTS:-4}
+        $extended
+        $debug
+        $verbose
+        --output_file $output
+        $fastq
+    ]]>    </command>
+
+    <inputs>
+        <param name="fastq" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" label="Uncorrected long reads"/>
+        <conditional name="cas_input">
+            <param name="cas_select" type="select" label="CAS file">
+                <option selected="true" value="bundle">Use bundled CAS file</option>
+                <option value="history">Use a fasta file in the history</option>
+            </param>
+                <when value="history">
+                    <param name="cas_file" type="data" format="fasta,fasta.gz" label="Select a CAS file"/>
+                </when>
+            </conditional>
+            <param name="technology" type="select" optional="false" label="Sequencing technology">
+                <option value="map-ont">map-ont</option>
+                <option value="map-pb">map-pb</option>
+                <option value="ava-ont">ava-ont</option>
+                <option value="ava-pb">ava-pb</option>
+            </param>
+            <param name="extended" argument="--extended_results" type="boolean" truevalue="--extended_results" falsevalue="" checked="false" label="Output extended results" />
+            <param name="gene_start_offset" argument="--gene_start_offset" type="integer" min="0" value="30" label="Only count CRISPR reads which cover this base"/>
+            <param name="min_mapping_quality" argument="--min_mapping_quality" type="integer" min="0" value="10" label="Minimum mapping quality score"/>
+            <param name="qcov_margin" argument="--qcov_margin" type="integer" min="0" value="100" label="Maximum perc coverage difference between CRISPR and read"/>
+            <param name="min_bitscore" argument="--min_bitscore" type="integer" min="0" value="38" label="Minimum blast bitscore"/>
+            <param name="min_identity" argument="--min_identity" type="integer" min="0" value="95" label="Minimum blast identity"/>
+            <param name="debug" type="boolean" truevalue="--debug" falsevalue="" checked="false" label="Turn on debugging" />
+            <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Turn on verbose output" />
+        </inputs>
+        <outputs>
+            <data name="output" format="tabular" label="${tool.name} on ${on_string} Output"/>
+            <data name="log" format="text" label="${tool.name} on ${on_string} Log">
+                <filter>debug is True</filter>
+            </data>
+        </outputs>
+
+        <help><![CDATA[
+
+    Documentation can be found at `<https://github.com/quadram-institute-bioscience/galru>`_.
+
+    ]]>        </help>
+    <citations>
+        <citation type="doi">10.1101/2020.05.31.126490v1</citation>
+    </citations>
+    </tool>