diff asmplot.xml @ 0:f4ab1b067529 draft

planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit a3bca7925574e058336e55d80e8390e95af770a7

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/asmplot.xml	Tue Feb 25 13:35:13 2025 +0000
@@ -0,0 +1,108 @@
+<tool id="merquryfk_asmplot" name="MerquryFK ASMplot" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
+    <description>Analyzes k-mer spectra for unique, shared, and missing k-mers</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        #set ASSEMBLY1="assembly."+$assembly_1.ext
+        ln -s '$reads' assembly.ktab &&
+        ln -s '$assembly_1' $ASSEMBLY1 &&
+        #if $assembly_2:
+            #set ASSEMBLY2="assembly2."+$assembly_2.ext
+            ln -s '$assembly_2' $ASSEMBLY2 &&
+        #end if
+        ln -s '$fastk_ktab_files' ktab_files.tar.gz &&
+        tar -xf ktab_files.tar.gz -C '.' &&
+        ASMplot
+        @PLOTS@
+        @MEASURE@
+        @GRAPHS@
+        $pdf
+        -T\${GALAXY_SLOTS:-1}
+        assembly.ktab
+        '$ASSEMBLY1'
+        #if $assembly_2:
+            $ASSEMBLY2
+        #end if
+        asmplot 
+    ]]></command>
+    <inputs>
+        <param name="reads" type="data" format="fastk_ktab" label="K-mer table (ktab) obtained from FastK tool"/>
+        <param name="fastk_ktab_files" type="data" format="fastk_ktab_tar" label="Select the TAR file consisting of all intermediate Ktab file from FastK"/>
+        <param name="assembly_1" type="data" format="fasta,fasta.gz" label="Assembly of genome" help="Must be same genome as the K-mer table was generated from"/>
+        <param name="assembly_2" type="data" format="fasta,fasta.gz" label="Additional assembly file" optional="true" help="Additional genome against which to compare"/>
+        <expand macro="plots"/>
+        <expand macro="sizes"/>
+        <expand macro="graphs"/>
+        <expand macro="pdf"/>
+    </inputs>
+    <outputs>
+        <collection name="outputs_png" type="list" label="${tool.name} on ${on_string}: PNG figures">
+            <filter>pdf is not True</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*).png" format="png"/>
+        </collection>
+        <collection name="outputs_pdf" type="list" label="${tool.name} on ${on_string}: PDF figures">
+            <filter>pdf is True</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*).pdf" format="pdf"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="reads" value="assembly.ktab"/>
+            <param name="fastk_ktab_files" ftype="fastk_ktab_tar" location="https://zenodo.org/records/14905247/files/asmplot_ktab.tar.gz"/>
+            <param name="assembly_1" value="assembly.fasta.gz"/>
+            <param name="width" value="6.0"/>
+            <param name="height" value="4.5"/>
+            <param name="graphs" value="-l,-f,-s"/>
+            <param name="pdf" value="False"/>
+            <conditional name="measure">
+                <param name="measurement" value="absolute"/>
+                <param name="max_x" value="2"/>
+                <param name="max_y" value="1"/>
+            </conditional>
+            <output_collection name="outputs_png" type="list" count="3"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="reads" value="assembly.ktab"/>
+            <param name="fastk_ktab_files" ftype="fastk_ktab_tar" location="https://zenodo.org/records/14905247/files/asmplot_ktab.tar.gz"/>
+            <param name="assembly_1" value="assembly.fasta.gz"/>
+            <param name="assembly_2" value="assembly_2.fasta.gz"/>
+            <param name="width" value="6.0"/>
+            <param name="height" value="4.5"/>
+            <param name="graphs" value="-l,-f,-s"/>
+            <param name="pdf" value="False"/>
+            <conditional name="measure">
+                <param name="measurement" value="absolute"/>
+                <param name="max_x" value="2"/>
+                <param name="max_y" value="1"/>
+            </conditional>
+            <output_collection name="outputs_png" type="list" count="3"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="reads" value="assembly.ktab"/>
+            <param name="fastk_ktab_files" ftype="tar" location="https://zenodo.org/records/14905247/files/asmplot_ktab.tar.gz"/>
+            <param name="assembly_1" value="assembly.fasta.gz"/>
+            <param name="assembly_2" value="assembly_2.fasta.gz"/>
+            <param name="width" value="6.0"/>
+            <param name="height" value="4.5"/>
+            <param name="graphs" value="-l,-f,-s"/>
+            <param name="pdf" value="True"/>
+            <conditional name="measure">
+                <param name="measurement" value="absolute"/>
+                <param name="max_x" value="2"/>
+                <param name="max_y" value="1"/>
+            </conditional>
+            <output_collection name="outputs_pdf" type="list" count="3"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        ASMplot looks at the spectra of the k-mers that:
+        (a) are in neither genome assembly file or the additional assembly file, 
+        (b) in genome assembly file but not the additional assembly file, 
+        (c) in the additional assembly file but not genome assembly file, and 
+        (d) in both genome assembly file and the additional assembly file. 
+        If the second assembly file is missing, then it looks at the spectra of the read k-mers that are and are not in the first assembly file.
+    ]]></help>
+    <expand macro="citation"/>
+</tool>
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