diff macros.xml @ 4:a315c25dc813 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Oct 12 19:07:05 2021 +0000
@@ -0,0 +1,86 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.2.5</token>
+    <token name="@VERSION_SUFFIX@">4</token>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">purge_dups</xref>
+        </xrefs>
+    </xml>
+    <xml name="trimmers">
+        <section name="section_hist" title="Histogram plot options" >
+            <!--<param name="cutoffs_his" type="data" optional="true" format="txt" label="Read depth cutoffs file" />-->
+            <param argument="--ymin" type="integer" optional="true" min="0" label="Specify a minimum for the Y axis"/>
+            <param argument="--ymax" type="integer" optional="true" label="Specify a maximum for the Y axis"/>
+            <param argument="--xmin" type="integer" optional="true" min="0" label="Specify a minimum for the X axis"/>
+            <param argument="--xmax" type="integer" optional="true" label="Specify a maximum for the X axis"/>
+            <param argument="--title" type="text" value="Read depth histogram plot" label="Histogram title"/>
+        </section>
+    </xml>
+    <token name="@HIST_PLOT@"><![CDATA[
+        python '$__tool_directory__/hist_plot.py' 
+        --cutoffs cutoffs.tsv
+        #if $function_select.section_hist.ymin
+            --ymin $function_select.section_hist.ymin
+        #end if
+        #if $function_select.section_hist.ymax
+            --ymax $function_select.section_hist.ymax
+        #end if
+        #if $function_select.section_hist.xmin
+            --xmin $function_select.section_hist.xmin
+        #end if
+        #if $function_select.section_hist.xmax
+            --xmax $function_select.section_hist.xmax
+        #end if
+        #if $function_select.section_hist.title
+            --title '${function_select.section_hist.title}'
+        #end if
+        depth.stat hist.png
+    ]]></token>
+    <token name="@CALCUTS@"><![CDATA[
+        calcuts
+        #if $function_select.section_calcuts.min_depth:
+            -f $function_select.section_calcuts.min_depth
+        #end if
+        #if $function_select.section_calcuts.low_depth:
+            -l $function_select.section_calcuts.low_depth
+        #end if
+        #if $function_select.section_calcuts.transition:
+            -m $function_select.section_calcuts.transition
+        #end if
+        #if $function_select.section_calcuts.upper_depth:
+            -u $function_select.section_calcuts.upper_depth
+        #end if
+        $function_select.section_calcuts.ploidy
+    ]]></token>
+    <xml name="calcuts">
+        <section name="section_calcuts" title="Calcuts options" expanded="true">
+            <param argument="-f" name="min_depth" type="float"  min="0" max="1" value="0.1" label="Minimum depth count fraction to maximum depth count"/>
+            <param argument="-l" name="low_depth" type="integer" min="0" optional="true" label="Lower bound for read depth" />
+            <param argument="-m" name="transition"  type="integer" min="0" optional="true" label="Transition between haploid and diploid"/>
+            <param argument="-u" name="upper_depth"  type="integer"  min="0" optional="true" label="Upper bound for read depth" />
+            <param name="ploidy" argument="-d" type="select" label="Ploidy" help="Treat as haploid assembly or diploid assembly">
+                <option value="-d 0" selected="true">Diploid</option>
+                <option value="-d 1">Haploid</option>
+            </param>
+        </section>
+    </xml>
+    <xml name="output_macro">
+        <param name="output_options" type="select" multiple="true" display="checkboxes" label="Output files">
+            <yield />
+            <option value="histogram" selected="true">Histogram plot</option>
+            <option value="calcuts_cutoff" selected="true">Calcuts cutoff</option>
+            <option value="calcuts_log">Calcuts log</option>
+        </param>
+    </xml>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">purge_dups</requirement>
+            <requirement type="package" version="3.4.2">matplotlib-base</requirement>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/bioinformatics/btaa025</citation>
+        </citations>
+    </xml>
+</macros>