# HG changeset patch
# User dfornika
# Date 1580495321 0
# Node ID d43117b98027bb05a159fa9d89cfbac33aad1feb

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/confindr/ commit 9e41ac63171c3e3a6fd2b4d018d0c60c9f1fbae1"

diff -r 000000000000 -r d43117b98027 confindr.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/confindr.xml	Fri Jan 31 18:28:41 2020 +0000
@@ -0,0 +1,80 @@
+<tool id="confindr" name="ConFindr" version="@VERSION@+galaxy0">
+    <description>
+        Intra-species bacterial contamination detection
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+
+    <command detect_errors="exit_code"><![CDATA[
+        #if str( $reads_input.reads_input_selector ) == "paired"
+          ln -s '$reads_input.reads_1' 'input/reads_R1.fastq.gz' &&
+          ln -s '$reads_input.reads_2' 'input/reads_R2.fastq.gz' &&
+        #end if
+        #if str( $reads_input.reads_input_selector ) == "paired_collection"
+          ln -s '$reads_input.reads.forward' 'input/reads_R1.fastq.gz' &&
+          ln -s '$reads_input.reads.reverse' 'input/reads_R2.fastq.gz' &&
+        #end if
+        
+        confindr.py 
+          --input_directory input \
+          --output_name output \
+
+    ]]></command>
+
+    <inputs>
+        <conditional name="reads_input">
+            <param name="reads_input_selector" type="select" label="Paired-end reads or paired collection" help="Select between paired and paired collection">
+                <option value="paired">Paired</option>
+                <option value="paired_collection">Paired Collection</option>
+            </param>
+            <when value="paired">
+                <param name="reads_1" type="data" format="@INTYPES@" label="Select first set of reads" help="Specify dataset with forward reads"/>
+                <param name="reads_2" type="data" format="@INTYPES@" label="Select second set of reads" help="Specify dataset with reverse reads"/>
+            </when>
+            <when value="paired_collection">
+                <param name="reads" format="@INTYPES@" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
+            </when>
+        </conditional>
+    </inputs>
+
+    <outputs>
+        <data name="report" format="tabular" from_work_dir="output/confindr_report.csv" label="${tool.name} on ${on_string} report file" />
+    </outputs>
+
+    <tests>
+        
+
+    </tests>
+
+    <help><![CDATA[
+**What it does**
+
+
+
+**Output**
+
+ConFindr will produce a tab-seperated output file with the following outputs:
+
++---------------+------------------------------------------------+
+|  Column       | Description                                    |
++===============+================================================+
+|               |                                                |
++---------------+------------------------------------------------+
+|               |                                                |
++---------------+------------------------------------------------+
+|               |                                                |
++---------------+------------------------------------------------+
+
+
+**Example Output**
+
+::
+
+
+    ]]></help>
+
+    <expand macro="citations"/>
+</tool>
diff -r 000000000000 -r d43117b98027 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Jan 31 18:28:41 2020 +0000
@@ -0,0 +1,34 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">confindr</requirement>
+            <yield />
+        </requirements>
+    </xml>
+
+    <xml name="version_command">
+        <version_command><![CDATA[confindr.py --version]]></version_command>
+    </xml>
+
+    <token name="@VERSION@">0.7.2</token>
+
+    <token name="@INTYPES">
+        fastq.gz,fastqsanger.gz
+    </token>
+
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @article{low2019confindr,
+                title={ConFindr: rapid detection of intraspecies and cross-species contamination in bacterial whole-genome sequence data},
+                author={Low, Andrew J and Koziol, Adam G and Manninger, Paul A and Blais, Burton and Carrillo, Catherine D},
+                journal={PeerJ},
+                volume={7},
+                pages={e6995},
+                year={2019},
+                publisher={PeerJ Inc.}
+                }
+            </citation>
+        </citations>
+    </xml>
+</macros>