changeset 6:47035d167365 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 558d30ff047fe2f62658e8b57e27ebe8db77ede1"

--- a/samtools_stats.xml	Mon Jul 29 08:49:54 2019 -0400
+++ b/samtools_stats.xml	Fri Sep 06 11:23:05 2019 -0400
@@ -1,12 +1,9 @@
-<tool id="samtools_stats" name="Samtools stats" version="2.0.2+galaxy1">
+<tool id="samtools_stats" name="Samtools stats" version="2.0.2+galaxy2">
     <description>generate statistics for BAM dataset</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <requirement type="package" version="5.2.3">gnuplot</requirement>
-        <requirement type="package" version="5.26">perl</requirement>
-    </expand>
+    <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
@@ -71,11 +68,6 @@
             @REGIONS_MANUAL@
             > '$output'
 
-            #if $cond_plot.select_plot=='yes':
-                && plot-bamstats '$output' $cond_plot.log -p '${html_file.files_path}'/
-                && mv '${html_file.files_path}'/index.html '${html_file}'
-            #end if
-
             #if $split_output_cond.split_output_selector == "yes":
                 #set outputs_to_split = str($split_output_cond.generate_tables).split(',')
                 && mkdir split
@@ -186,16 +178,6 @@
         <param name="sparse" argument="-x/--sparse" type="boolean" truevalue="-x" falsevalue="" checked="False" label="Suppress absence of insertions" help="Suppress outputting IS rows where there are no insertions."/>
         <param name="remove_overlaps" argument="-p/--remove-overlaps" type="boolean" truevalue="-p" falsevalue="" checked="False" label="Remove overlaps of paired-end reads from coverage and base count computations" />
         <param name="cov_threshold" argument="-g/--cov-threshold"  optional="true" type="integer" label="Only bases with coverage above this value will be included in the target percentage computation" />
-        <conditional name="cond_plot">
-            <param name="select_plot" type="select" label="Generate plots with plot-bamstats">
-                <option value="no" selected="True">No</option>
-                <option value="yes">Yes</option>
-            </param>
-            <when value="no"/>
-            <when value="yes">
-                <param name="log" argument="-l/--log-y" type="boolean" truevalue="-l" falsevalue="" checked="False" label="log scale insert size plot" help="Set the Y axis scale of the Insert Size plot to log 10"/>
-            </when>
-        </conditional>
     </inputs>
 
     <outputs>
@@ -207,9 +189,6 @@
             <discover_datasets directory="split" pattern="(?P&lt;designation&gt;.+)\.tab" format="tabular" visible="false"/>
             <filter>split_output_cond['split_output_selector'] == 'yes'</filter>
         </collection>
-        <data format="html" name="html_file" label="${tool.name} on ${on_string}: plot-bamstats">
-            <filter>cond_plot['select_plot']=='yes'</filter>
-        </data>
     </outputs>
     <tests>
         <!-- https://github.com/samtools/samtools/blob/9ce8c64493f7ea3fa69bc5c1ac980b1a8e3dcf1f/test/test.pl#L2402 -->
@@ -360,9 +339,6 @@
                 <param name="addref_select" value="history" />
                 <param name="ref" value="samtools_stats_ref.fa" ftype="fasta" />
             </conditional>
-            <conditional name="cond_plot">
-                <param name="select_plot" value="yes"/>
-            </conditional>
             <output name="output" file="samtools_stats_out1.tab" ftype="tabular" lines_diff="2" />
         </test>
         <test>
@@ -386,6 +362,8 @@
 **What it does**
 
 This tool runs the ``samtools stats`` command.
+
+The results of samtools stats can be visualized with MultiQC (for this the default of a single output file needs to be selected).
     ]]></help>
     <expand macro="citations"/>
 </tool>