--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/omark.xml	Fri Mar 14 10:03:31 2025 +0000
@@ -0,0 +1,127 @@
+<?xml version="1.0"?>
+<tool id="omark" name="OMArk" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>proteome quality assessment</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">omark</xref>
+    </xrefs>
+    <requirements>
+        <expand macro="requirements" />
+    </requirements>
+
+    <command detect_errors="exit_code"><![CDATA[
+    omamer search --db '$database.fields.path' --query '$input' --out 'output_omamer'
+
+    &&
+
+    omark
+    -f 'output_omamer'
+    -d '$database.fields.path'
+    $omark_mode
+
+    #if $input_iso:
+        -i '$input_iso'
+    #end if
+
+    #if $t:
+        -t '$t'
+    #end if
+
+    #if $r:
+        -r '$r'
+    #end if
+
+    -o omark_galaxy
+    ]]></command>
+
+    <inputs>
+        <param name="input" type="data" format="fasta" label="Protein sequences"/>
+        <param name="input_iso" type="data" format="txt" optional="true" label="Input isoform file" help="A semi-colon separated file, listing all isoforms of each genes, with one gene per line."/>
+        <param argument="-c" name="omark_mode" type="boolean" checked="false" truevalue="-c" falsevalue="" label="Only compute a list of conserved HOGs" help="Can be used to obtain a set of genes on which to train"/>
+        <param name="database" label="OMAmer database" type="select">
+            <options from_data_table="omamer"/>
+        </param>
+
+        <param argument="-t" type="text" optional="true" label="Taxonomic identifier" help="NCBI taxid corresponding to the input proteome">
+            <sanitizer invalid_char="">
+                <valid initial="string.letters,string.digits">
+                    <add value="_" />
+                </valid>
+            </sanitizer>
+            <validator type="regex">[0-9a-zA-Z_]+</validator>
+        </param>
+        <param argument="-r" type="text" optional="true" label="Taxonomic rank">
+            <sanitizer invalid_char="">
+                <valid initial="string.letters,string.digits">
+                    <add value="_" />
+                </valid>
+            </sanitizer>
+            <validator type="regex">[0-9a-zA-Z_]+</validator>
+        </param>
+
+        <param name="outputs" type="select" multiple="true" label="Which outputs should be generated">
+            <option value="detail_sum" selected="true">Detailed summary</option>
+            <option value="hog">HOG identifiers</option>
+            <option value="pdf">PDF Graphic representation </option>
+            <option value="png">PNG Graphic representation </option>
+            <option value="sum">Comparative proteome analysis</option>
+            <option value="tax">Taxomony</option>
+            <option value="ump">Protein identifiers</option>
+        </param>
+    </inputs>
+
+    <outputs>
+        <data name="omark_detail_sum" format="txt" label="${tool.name} on ${on_string}: Detailed summary" from_work_dir="omark_galaxy/*detailed_summary.txt">
+            <filter>outputs and 'detail_sum' in outputs</filter>
+        </data>
+        <data name="omark_hog" format="omq" label="${tool.name} on ${on_string}: HOG identifiers" from_work_dir="omark_galaxy/*.omq">
+            <filter>outputs and 'hog' in outputs</filter>
+        </data>
+        <data name="omark_pdf" format="pdf" label="${tool.name} on ${on_string}: Graphic representation (pdf)" from_work_dir="omark_galaxy/*.pdf">
+            <filter>outputs and 'pdf' in outputs</filter>
+        </data>
+        <data name="omark_png" format="png" label="${tool.name} on ${on_string}: Graphic representation (png)" from_work_dir="omark_galaxy/*.png">
+            <filter>outputs and 'png' in outputs</filter>
+        </data>
+        <data name="omark_sum" format="sum" label="${tool.name} on ${on_string}: Comparative proteome analysis" from_work_dir="omark_galaxy/*.sum">
+            <filter>outputs and 'sum' in outputs</filter>
+        </data>
+        <data name="omark_tax" format="txt" label="${tool.name} on ${on_string}: Taxomony" from_work_dir="omark_galaxy/*.tax">
+            <filter>outputs and 'tax' in outputs</filter>
+        </data>
+        <data name="omark_ump" format="ump" label="${tool.name} on ${on_string}: Protein identifiers" from_work_dir="omark_galaxy/*.ump">
+            <filter>outputs and 'ump' in outputs</filter>
+        </data>
+    </outputs>
+
+    <tests>
+        <test expect_failure="true">
+            <param name="input" value="input.fasta"/>
+            <param name="outputs" value="sum,detail_sum,png,hog,pdf,ump,tax"/>
+            <param name="database" value="test"/>
+
+            <!-- Couldn't create a minimal working hdf5 dataset -->
+            <assert_stderr>
+                <has_text text="file signature not found"/>
+                <has_text text="End of HDF5 error back trace" />
+            </assert_stderr>
+        </test>
+    </tests>
+
+
+    <help><![CDATA[
+        OMark_: is a software for proteome quality assessment.
+        It provides measures of proteome completeness, characterizes the consistency
+        of all protein coding genes with regard to their homologs, and identifies the
+        presence of contamination from other species.
+
+        OMArk relies on the OMA orthology database.
+        For more information, please refer to the OMamer_ documentaion.
+
+        .. _OMark: https://github.com/DessimozLab/OMArk
+        .. _OMamer: https://github.com/DessimozLab/omamer
+    ]]></help>
+    <expand macro="citation"/>
+</tool>