--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MergeSTR/mergeSTR.xml	Sat Apr 23 16:34:03 2022 +0000
@@ -0,0 +1,171 @@
+<?xml version="1.0" ?>
+<tool id="mergeSTR" name="MergeSTR" version="@tool_version@">
+     <description>MergeSTR merges multiple VCF files produced by the same TR
+        genotyper into a single VCF file.
+    </description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="requirements"/>
+    <version_command>mergeSTR --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+    @INDEX_VCFS@
+    #set $inputs = [str(vcf['vcf']) for vcf in $required_arguments.vcfs]
+    #set $temp_inputs = $get_new_vcf_names($inputs)
+    #set $indexed_inputs_comma_separated = ",".join($temp_inputs)
+
+    $index_vcfs($inputs, $temp_inputs)
+
+    mergeSTR
+
+## vcfs definition
+#if $required_arguments.vcfs:
+   --vcfs $indexed_inputs_comma_separated
+#end if
+## end vcfs definition
+## out definition
+#if $required_arguments.out:
+   --out $required_arguments.out
+#end if
+## end out definition
+## vcftype definition
+#if $required_arguments.vcftype:
+   --vcftype $required_arguments.vcftype
+#end if
+## end vcftype definition
+## update_sample_from_file definition
+#if $special_merge_options.update_sample_from_file:
+   --update-sample-from-file
+#end if
+## end update_sample_from_file definition
+## verbose definition
+#if $optional_arguments.verbose:
+   --verbose
+#end if
+## end verbose definition
+## quiet definition
+#if $optional_arguments.quiet:
+   --quiet
+#end if
+## end quiet definition
+## version definition
+#if $versione869.version:
+   --version
+#end if
+## end version definition
+1>$stdout 2>$stderr
+]]></command>
+
+
+    <inputs>
+        <section name="required_arguments" title="Required arguments"
+                 expanded="false">
+            <repeat name="vcfs" title="VCF files to merge">
+                <param argument="--vcf" type="data" format="vcf_bgzip" label="VCF file" help="VCF file to analyze"/>
+            </repeat>
+            <param argument="--out" type="text" optional="false" label="out"
+                   help="Prefix to name output files"/>
+            <param argument="--vcftype" type="select" optional="true"
+                   label="vcftype"
+                   help="Genotyper that was used to create this VCF input">
+                <expand macro="vcfTypes"/>
+            </param>
+        </section>
+        <section name="special_merge_options" title="Special merge options"
+                 expanded="false">
+            <param argument="--update-sample-from-file" type="boolean"
+                   optional="true" label="update_sample_from_file"
+                   help="Use file names, rather than sample header names, when merging"/>
+        </section>
+        <section name="optional_arguments" title="Optional arguments"
+                 expanded="false">
+            <param argument="--verbose" type="boolean" optional="true"
+                   label="verbose" help="Print out extra info"/>
+            <param argument="--quiet" type="boolean" optional="true"
+                   label="quiet" help="Don't print out anything"/>
+        </section>
+        <section name="versione869" title="Version" expanded="false">
+            <param argument="--version" type="boolean" optional="true"
+                   label="version"
+                   help="show program's version number and exit"/>
+        </section>
+    </inputs>
+
+
+    <outputs>
+        <data name="stdout" label="STDOUT and output files" format="txt">
+            <discover_datasets format="vcf" pattern="(?P&lt;designation&gt;.+)\.vcf$" visible="true"/>
+        </data>
+        <data name="stderr" label="STDERR output" format="txt"/>
+    </outputs>
+
+
+    <tests>
+        <section name="main_params">
+            <param name="out" value="test_result"/>
+            <param name="vcftype" value="hipstr"/>
+            <repeat name="vcfs">
+                <param name="vcf" value="NA12878_chr21_hipstr.sorted.vcf.gz"/>
+            </repeat>
+            <repeat name="vcfs">
+                <param name="vcf" value="NA12891_chr21_hipstr.sorted.vcf.gz"/>
+            </repeat>
+        </section>
+        <section name="other">
+            <param name="verbose" value="true"/>
+        </section>
+        <output name="stdout" file="stdout.txt">
+            <discovered_dataset designation="test_result">
+                <!-- The vcf output itself can't be directly compared, because it contains the command that executed it, and that command is different for every run -->
+                <assert_contents>
+                    <has_size value="3106028" delta="100"/>
+                    <has_text text="##fileformat=VCFv4.1"/>
+                    <has_n_lines n="9695"/>
+                </assert_contents>
+            </discovered_dataset>
+        </output>
+        <output name="stderr" file="stderr.txt"/>
+    </tests>
+
+
+    <help>usage: main.py [-h] --vcfs VCFS --out OUT [--vcftype VCFTYPE]
+        [--update-sample-from-file] [--verbose] [--quiet] [--version]
+
+        options:
+        -h, --help show this help message and exit
+
+        Required arguments:
+        --vcfs VCFS Comma-separated list of VCF files to merge (must be sorted,
+        bgzipped and indexed)
+        --out OUT Prefix to name output files
+        --vcftype VCFTYPE ##!!## Name trh could not be loaded
+
+        Special merge options:
+        --update-sample-from-file
+        Use file names, rather than sample header names, when merging
+
+        Optional arguments:
+        --verbose Print out extra info
+        --quiet Don't print out anything
+
+        Version:
+        --version show program's version number and exit
+    </help>
+
+
+    <citations>
+        <citation type="bibtex">@misc{TRTools: a toolkit for genome-wide
+            analysis of tandem repeats,
+            author = {Nima Mousavi, Jonathan Margoliash, Neha Pusarla, Shubham
+            Saini, Richard Yanicky, Melissa Gymrek},
+            year = {2020},
+            title = {TRTools},
+            publisher = {GitHub},
+            journal = {GitHub repository},
+            url = {https://github.com/gymreklab/trtools},
+            }
+        </citation>
+    </citations>
+</tool>