--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/virheat.xml	Wed May 15 13:37:49 2024 +0000
@@ -0,0 +1,185 @@
+<tool id="virheat" name="VirHEAT: visualize allele frequencies"
+      version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
+      profile="@PROFILE@">
+    <description>
+        from VCFs as a heatmap and map mutations to respective genes
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="biotools"/>
+    <expand macro="requirements"/>
+    <expand macro="version"/>
+    <command detect_errors="exit_code"><![CDATA[
+#import re
+#set $vcfs_dir = 'vcfs_dir/'
+mkdir -p $vcfs_dir &&
+mkdir -p ./output_dir &&
+#set $outfile = 'tmp_output.' + str($advanced.output_type)
+#for $input_file in $sinputs
+    #set $file_path = $vcfs_dir + re.sub('[^\s\w\-\\.]', '_', str($input_file.element_identifier))
+    ln -s '$input_file' '$file_path' &&
+#end for
+#set $output_dir = 'output_dir/'
+virheat
+    '$vcfs_dir'
+    '$output_dir'
+    --name '$outfile'
+    #if $genome_data.choice == 'length'
+        -l $genome_data.genome_length
+    #else
+        -g '$genome_data.gff3_file'
+    #end if
+    #if $varfreq
+        -t $varfreq
+    #end if
+    $delete
+    -n $delete_n
+    #if $zoom.choice == 'yes'
+        -z $zoom.zoom_start $zoom.zoom_stop
+    #end if
+    $sort
+    --min-cov $min_cov
+    ]]></command>
+    <inputs>
+        <param name="sinputs" type="data_collection" format="vcf" label="Variant lists data" help="Select at least two datasets (or a dataset collection) with variant lists. Datasets are expected to represent individual samples and dataset names will be used as sample identifiers." multiple="true" collection_type="list" />
+        <conditional name="genome_data">
+            <param name="choice" type="select"
+                   label="Data for genomic annotation">
+                <option value="length">length of the genome</option>
+                <option value="gff3">gff3 file</option>
+            </param>
+            <when value="length">
+                <param name="genome_length" argument="-l" type="integer" min="0" label="Genome length"/>
+            </when>
+            <when value="gff3">
+                <param name="gff3_file" argument="-g" type="data" format="gff3" label="GFF3 file" help="GFF3 file contains annotations for the genome and allows to display genes harboring a mutation. Ensure that the file follows the GFF3 specification."/>
+            </when>
+        </conditional>
+        <param name="varfreq" argument="-t" type="float" min="0" max="1" value="0" optional="true" label="Variant Frequency Threshold" help="Only plot variants with an intrasample frequency above this threshold in at least one sample." />
+        <param argument="--delete" type="boolean" truevalue="--delete" falsevalue="--no-delete" checked="true" label="Delete mutations that are present in all samples and their maximum frequency divergence is smaller than 0.5"/>
+        <param name="delete_n" argument="-n" type="integer" min="0" value="0" label="Do not show mutations that occur n times or less"/>
+        <conditional name="zoom">
+            <param name="choice" type="select" label="Restrict the plot to a specific genomic region">
+                <option value="yes">Yes</option>
+                <option value="no">No</option>
+            </param>
+            <when value="yes">
+                <param name="zoom_start" type="integer" label="Start"/> 
+                <param name="zoom_stop" type="integer" label="End"/>
+            </when>
+            <when value="no"/>
+        </conditional>
+        <param argument="--sort" type="boolean" truevalue="--sort" falsevalue="--no-sort" checked="false" label="Sort sample names alphanumerically"/>
+        <param argument="--min-cov" type="integer" min="1" max="1000" value="20" label="Display mutations covered at least x time"/>
+        <section name="advanced" title="Image Properties" expanded="true">
+            <param name="output_type" type="select" label="Plot output format" >
+                <option value="pdf" selected="true" >PDF</option>
+                <option value="png" >PNG</option>
+                <option value="svg">SVG</option>
+                <option value="tiff" >TIFF</option>
+                <option value="bmp" >BMP</option>
+                <option value="jpeg" >JPEG</option>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="pdf" from_work_dir="output_dir/tmp_output.*"
+            label="Variant-Frequency Plot on ${on_string}: ${advanced.output_type}">
+            <change_format>
+                <when input="advanced.output_type" value="svg" format="svg" />
+                <when input="advanced.output_type" value="png" format="png" />
+                <when input="advanced.output_type" value="tiff" format="tiff" />
+                <when input="advanced.output_type" value="bmp" format="bmp" />
+                <when input="advanced.output_type" value="jpeg" format="jpg" />
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <!-- test1: gff3, pdf -->
+            <param name="sinputs" value="day_0.vcf,day_2.vcf,day_4.vcf,day_18.vcf,day_26.vcf,day_32.vcf,day_47.vcf,day_55.vcf,day_60.vcf,day_76.vcf,day_83.vcf,day_85.vcf,day_91.vcf,day_96.vcf,day_100.vcf,day_103.vcf,day_111.vcf"/>
+            <conditional name="genome_data">
+                <param name="choice" value="gff3"/>
+                <param name="gff3_file" value="SARS-CoV-2.gff3"/>
+            </conditional>
+            <conditional name="zoom">
+                <param name="choice" value="yes"/>
+                <param name="zoom_start" value="22599"/>
+                <param name="zoom_stop" value="23278"/>
+            </conditional>
+            <output name="outfile" ftype="pdf">
+                <assert_contents>
+                    <has_text text="day"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <!-- test2: length, svg -->
+            <param name="sinputs" value="day_76.vcf,day_83.vcf,day_91.vcf,day_103.vcf" ftype="vcf" />
+            <conditional name="genome_data">
+                <param name="choice" value="length"/>
+                <param name="genome_length" value="29903"/>
+            </conditional>
+            <conditional name="zoom">
+                <param name="choice" value="yes"/>
+                <param name="zoom_start" value="22599"/>
+                <param name="zoom_stop" value="23278"/>
+            </conditional>
+            <output name="outfile" ftype="svg">
+                <assert_contents>
+                    <has_text text="day"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <!-- test3: gff3, threshold, png, delete, delete-n -->
+            <param name="sinputs" value="day_76.vcf,day_83.vcf,day_91.vcf,day_103.vcf" ftype="vcf" />
+            <param name="varfreq" value="0.1"/>
+            <param name="delete" value="yes"/>
+            <param name="delete_n" value="1"/>
+            <conditional name="genome_data">
+                <param name="choice" value="gff3"/>
+                <param name="gff3_file" value="SARS-CoV-2.gff3"/>
+            </conditional>
+            <conditional name="zoom">
+                <param name="choice" value="no"/>
+            </conditional>
+            <output name="outfile" ftype="png">
+                <assert_contents>
+                    <has_text text="day"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <!-- test4: length, zoom, sort, tiff -->
+            <param name="sinputs" value="day_0.vcf,day_2.vcf,day_4.vcf,day_18.vcf,day_26.vcf,day_32.vcf,day_47.vcf,day_55.vcf,day_60.vcf,day_76.vcf,day_83.vcf,day_85.vcf,day_91.vcf,day_96.vcf,day_100.vcf,day_103.vcf,day_111.vcf"/>
+            <param name="varfreq" value="0.1"/>
+            <param name="delete" value="false"/>
+            <param name="delete_n" value="0"/>
+            <param name="sort" value="true"/>
+            <param name="min_cov" value="25"/>
+            <conditional name="zoom">
+                <param name="choice" value="yes"/>
+                <param name="zoom_start" value="22599"/>
+                <param name="zoom_stop" value="23278"/>
+            </conditional>
+            <section name="advanced">
+                <param name="output_type" value="tiff"/>
+            </section>
+            <conditional name="genome_data">
+                <param name="choice" value="length"/>
+                <param name="genome_length" value="29903"/>
+            </conditional>
+            <output name="outfile">
+                <assert_contents>
+                    <has_text text="day"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_HEADER@
+    ]]></help>
+    <expand macro="citations"/>
+</tool>