changeset 8:99da8dc2b590 draft

planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ariba commit 067b5a6a02d5f04c2155b45eed5df257a1360645-dirty

--- a/ariba_summary.xml	Mon Feb 18 12:08:22 2019 -0500
+++ b/ariba_summary.xml	Wed Feb 20 10:26:18 2019 -0500
@@ -20,16 +20,78 @@
             ln -s '${input_file}' ${_input_file} &&
             #set $named_input_files = $named_input_files + ' ' + $_input_file
         #end for
-        ariba summary out $named_input_files
+        ariba summary out 
+        
+        --preset $options.preset
+        --cluster_cols $options.cluster_cols
+        
+        #if $options.col_filter
+            $options.col_filter
+        #end if
+
+        #if $options.no_tree
+            $options.no_tree
+        #end if
+
+        #if $options.row_filter
+            $options.row_filter
+        #end if
+
+        --min_id $options.min_id
+
+        #if $options.v_groups
+            $options.v_groups
+        #end if
+
+        #if $options.known_variants
+            $options.known_variants
+        #end if
+
+        #if $options.novel_variants
+            $options.novel_variants
+        #end if
+
+        $named_input_files
+        > $log
     ]]>    </command>
     <inputs>
-            <param name="ariba_reports" format="tabular,txt" type="data" label="Report (tsv) file from ARIBA run" help="This command requires one or more report tsv file generated by ARIBA run command."/>
+        <param name="ariba_reports" format="tabular,txt" type="data" multiple="true" label="Report (tsv) file from ARIBA run" help="This command requires one or more report tsv file generated by ARIBA run command."/>
+        <section name="options" title="Optional Arguments">
+                <param name="preset" type="select" label="Select a preset">
+                    <option value="minimal" selected="True">minimal</option>
+                    <option value="cluster_all">cluster all</option>
+                    <option value="cluster_var_groups">cluster var groups</option>
+                    <option value="all">all</option>
+                    <option value="all_no_filter">all no filter</option>
+                </param>
+                <param name="cluster_cols" type="select" multiple="true" display="checkboxes" label="Cluster columns" help="">
+                    <option value="assembled">assembled</option>
+                    <option value="match" selected="True">match</option>
+                    <option value="ref_seq">ref_seq</option>
+                    <option value="pct_id">pct_id</option>
+                    <option value="ctg_cov">ctg_cov</option>
+                    <option value="known_var">known_var</option>
+                    <option value="novel_var">novel_var</option>
+                </param>
+                <param argument="--col_filter" type="boolean" truevalue="--col_filter" falsevalue="" checked="true" label="Column filter" help="Choose whether columns where all values are No or
+                            NA are removed (Default:Yes)" />
+                <param argument="--no_tree" type="boolean" truevalue="--no_tree" falsevalue="" checked="false" label="Do not make phandango tree" help="" />
+                <param argument="--row_filter" type="boolean" truevalue="--row_filter" falsevalue="" checked="true" label="Row filter" help="Choose whether rows where all values are No or NA
+                            are removed (Default: Yes)" />
+                <param argument="--min_id" type="integer" value="90" label="Minimum percent identity cutoff to count as assembled" help="(Default: 90)"></param>
+                <param argument="--v_groups" type="boolean" truevalue="--v_groups" falsevalue="" checked="false" label="Show a group column for each group of variants" help="" />
+                <param argument="--known_variants" type="boolean" truevalue="--known_variants" falsevalue="" checked="false" label="Report all known variants" help="" />
+                <param argument="--novel_variants" type="boolean" truevalue="--novel_variants" falsevalue="" checked="false" label="Report all novel variants" help="" />
+        </section>
     </inputs>
 
     <outputs>
-        <data format="tabular" name="summary_csv" label="${tool.name} on ${on_string} report file" from_work_dir="out.tsv" />
-        <data format="tabular" name="phandango_csv" label="${tool.name} on ${on_string}: Phandango CSV" from_work_dir="out.phandango.csv"/>
-        <data format="text" name="phandango_tree" label="${tool.name} on ${on_string}: Phandango Tree file" from_work_dir="out.phandango.tre"/>
+        <data name="log" format="tabular"  label="${tool.name} on ${on_string} log file"/>
+        <data name="summary_csv" format="tabular"  label="${tool.name} on ${on_string} report file" from_work_dir="out.tsv" />
+        <data name="phandango_csv" format="tabular" label="${tool.name} on ${on_string}: Phandango CSV" from_work_dir="out.phandango.csv" />
+        <data name="phandango_tree" format="text" label="${tool.name} on ${on_string}: Phandango Tree file" from_work_dir="out.phandango.tre">
+            <filter>no_tree is False</filter>
+        </data>
     </outputs>
 
     <help><![CDATA[