diff bio_hansel.xml @ 6:5a42e475436e draft

planemo upload for repository https://github.com/phac-nml/bio_hansel commit e04f7d6043451f66946394d5a14582a1b39a6ec7-dirty

--- a/bio_hansel.xml	Wed Feb 21 12:13:32 2018 -0500
+++ b/bio_hansel.xml	Thu Feb 22 12:21:08 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="bio_hansel" name="Bio Hansel" version="1.2.0">
+<tool id="bio_hansel" name="Bio Hansel" version="1.2.1">
     <description>SNV Subtyping with genome assemblies or reads</description>
     <requirements>
         <requirement type="package" version="1.2.0">bio_hansel</requirement>
@@ -53,7 +53,7 @@
 
         ## Use Json output
         #if $dev_args.use_json == "yes":
-        	--json
+            --json
         #end if
 
         #if $kmer_vals.kmer_min
@@ -80,6 +80,10 @@
             --max-intermediate-tiles $qc_vals.max_intermediate_tiles
         #end if
 
+        #if $qc_vals.low_coverage_warning
+            --low-cov-warning $qc_vals.low_coverage_warning
+        #end if
+
         ## Adding more parameters to the command.
         -vvv -t "\${GALAXY_SLOTS:-1}" -o results.tab -O match_results.tab -S tech_results.tab
 
@@ -101,10 +105,8 @@
         
         #elif $data_type.type =="paired":
             -p '$data_type.fastq_input1.name'.fastq  '$data_type.fastq_input2.name'.fastq
-
         #end if
 
-
     ]]></command>
     <inputs>
         <conditional name="data_type">
@@ -147,26 +149,27 @@
             <param name="min_ambiguous_tiles" argument="--min-ambiguous-tiles" optional="True" type="integer" min="0" label="QC: Min number of tiles missing for Ambiguous Result" value="3" help="default = 3"/>
             <param name="max_missing_tiles" argument="--max-missing-tiles" optional="True" type="float" min="0" max="1" label="QC: Decimal Proportion of max allowed missing tiles" value="0.05" help="default = 0.05, valid values {0.0 - 1.0}"/>
             <param name="max_intermediate_tiles" argument="--max-intermediate-tiles" optional="True" type="float" min="0" max="1" label="QC: Decimal Proportion of max allowed missing tiles for an intermediate subtype" value="0.05" help="default = 0.05, valid values {0.0 - 1.0}"/> 
+            <param name="low_coverage_warning" argument="--low-cov-warning" optional="True" type="integer" min="0" label="QC: Overall tile coverage below this value will trigger a low coverage warning" value="20" help="default = 20"/> 
         </section>
         <section name="dev_args" title="Developer Options" expanded="False">
-        	<param name="use_json" type="select" label="Enable JSON output" help="Use this option of you need json representations of analysis' details">
-            	<option value="no">no</option>
-            	<option value="yes">yes</option>
-        	</param>
-    	</section>
+            <param name="use_json" type="select" label="Enable JSON output" help="Use this option of you need json representations of analysis' details">
+                <option value="no">no</option>
+                <option value="yes">yes</option>
+            </param>
+        </section>
     </inputs>
     <outputs>
         <data format="tabular" name="results.tab" from_work_dir="results.tab" label="results.tab"/>
         <data format="tabular" name="match_results.tab" from_work_dir="match_results.tab" label="match_results.tab"/>
         <data format="tabular" name="tech_results.tab" from_work_dir="tech_results.tab" label="tech_results.tab"/>
         <data format="json" name="results.json" from_work_dir="results.tab.json" label="results.json">
-        	<filter>dev_args['use_json'] == "yes"</filter>
-       	</data>
+            <filter>dev_args['use_json'] == "yes"</filter>
+        </data>
         <data format="json" name="match_results.json" from_work_dir="match_results.tab.json" label="match_results.json">
-        	<filter>dev_args['use_json'] == "yes"</filter>
+            <filter>dev_args['use_json'] == "yes"</filter>
         </data>
         <data format="json" name="tech_results.json" from_work_dir="tech_results.tab.json" label="tech_results.json">
-        	<filter>dev_args['use_json'] == "yes"</filter>
+            <filter>dev_args['use_json'] == "yes"</filter>
         </data>
     </outputs>
     <tests>
@@ -325,4 +328,4 @@
             }
         }</citation>
     </citations>
-</tool>
\ No newline at end of file
+</tool>