# HG changeset patch
# User dfornika
# Date 1574476512 0
# Node ID 481b5fc3a79aa7f49075dd4684f5d777513307b1

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit f07bc53dc1dffac1d5a7d93d5052d8b2b9c8ad5a-dirty"

diff -r 000000000000 -r 481b5fc3a79a tetyper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tetyper.xml	Sat Nov 23 02:35:12 2019 +0000
@@ -0,0 +1,83 @@
+<tool id="tetyper" name="TETyper" version="1.1+galaxy0">
+    <description></description>
+    <requirements>
+        <requirement type="package" version="1.1">tetyper</requirement>
+    </requirements>
+    <command detect_errors="exit_code">
+        <![CDATA[
+        TETyper.py
+            --threads \${GALAXY_SLOTS:-1}
+            #if $collection_paired.selector == "paired"
+                --fq1 '${collection_paired.forward_input}' --fq2'${collection_paired.reverse_input}'
+            #elif $collection_paired.selector == "collection":
+                --fq1 '${single_paired.input_pair.forward}' --fq2 '${single_paired.input_pair.reverse}'
+            #end if
+            --outprefix output
+        ]]>
+    </command>
+    <inputs>
+        <conditional name="collection_paired">
+            <param name="selector" type="select" label="Collection or paired reads" >
+                <option value="collection">Collection</option>
+                <option value="paired" selected="True">Paired</option>
+            </param>
+            <when value="collection">
+                <param format="fastq" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTQ datasets" />
+            </when>
+            <when value="paired">
+                <param format="fastq" name="forward_input" type="data" label="Forward strand" help="FASTQ dataset"/>
+                <param format="fastq" name="reverse_input" type="data" label="Reverse strand" help="FASTQ dataset"/>
+            </when>
+        </conditional>
+        <param name="reference" />
+        <param name="flank_length" />
+    </inputs>
+    <outputs>
+        <data name="summary" format="tabular" from_work_dir="output_summary.txt" label="${tool.name} on ${on_string} summary"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+      <![CDATA[
+**What it does**
+
+TETyper is designed for typing a specific transposable element (TE) of interest from paired-end sequencing data. It determines single nucleotide variants (SNVs) and deletions within the TE, as well as flanking sequences surrounding the TE.
+
+**Output**
+
+TETyper will produce a tab-seperated output file with the following outputs:
+
++---------------+------------------------------------------------+
+|  Column       | Description                                    |
++===============+================================================+
+|  Deletions    | A list of sequence ranges corresponding to regions of the reference classified as deletions for this sample, or "none" for no deletions. |
++---------------+------------------------------------------------+
+|  Structural_variant     |                                      |
++---------------+------------------------------------------------+
+|  SNPs_homozygous        |                                      |
++---------------+------------------------------------------------+
+|  SNPs_heterozygous          |                                  |
++---------------+------------------------------------------------+
+|  Heterozygous_SNP_counts         |                             |
++---------------+------------------------------------------------+
+|  SNP_variant     |                                             |
++---------------+------------------------------------------------+
+|  Combined_variant |                                            |
++---------------+------------------------------------------------+
+|  Left_flanks         |                                         |
++---------------+------------------------------------------------+
+|  Right_flanks    |                                             |
++---------------+------------------------------------------------+
+|  Left_flank_counts    |                                        |
++---------------+------------------------------------------------+
+|  Right_flank_counts     |                                      |
++---------------+------------------------------------------------+
+|  X_Y_presence    |                                             |
++---------------+------------------------------------------------+
+
+      ]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1099/mgen.0.000232</citation>
+    </citations>
+</tool>