diff gfastats.xml @ 3:8ccbf07a5433 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5

--- a/gfastats.xml	Wed Jun 01 15:15:57 2022 +0000
+++ b/gfastats.xml	Mon Jul 11 14:13:13 2022 +0000
@@ -54,12 +54,14 @@
                 --seq-report
                 $mode_condition.statistics_condition.out_sequence
             #end if
+            $mode_condition.discover_paths
             $mode_condition.tabular > '$stats'
         #else
             --agp-to-path $mode_condition.agp_to_path
             $mode_condition.discover_paths
             -o dataset.gfa
         #end if
+        --threads \${GALAXY_SLOTS:-8}
         #if $mode_condition.selector == 'manipulation' or $mode_condition.selector == 'scaffolding'
             && mv dataset* output_dataset
         #end if
@@ -155,7 +157,7 @@
                     </when>
                     <when value="coordinates">
                         <param argument="--out-coord" type="select" label="BED coordinares feature"
-                            help="Generates bed coordinates of given feature. Default: agp">
+                            help="Generates bed coordinates of given feature. Default: AGP">
                             <option value="a">AGP</option>
                             <option value="c">Contigs</option>
                             <option value="g">Gaps</option>
@@ -172,10 +174,12 @@
                 </conditional>
                 <param argument="--tabular" type="boolean" truevalue="--tabular" falsevalue="" checked="true"
                     label="Tabular-format output" help="Generate output in tabular format"/>
+                <param argument="--discover-paths" type="boolean" truevalue="--discover-paths" falsevalue="" checked="false" label="Generates the initial set of paths" help="In the graph space an assembly 
+                    is a collection of segment and edges/gaps between these segments. A path defines a potential walk through the segments and edges/gaps that corresponds to a hypothesis of the actual linear sequence" />
             </when>
             <when value="scaffolding">
                 <param argument="--agp-to-path" type="data" format="agp" label="Input AGP file" help="Integrate the AGP information into the assembly graph as paths. The scaffolding information is converted into paths through the graph" />
-                <param argument="--discover-paths" type="boolean" truevalue="--discover-paths" falsevalue="" checked="false" label="generates the initial set of paths" help="In the graph space an assembly 
+                <param argument="--discover-paths" type="boolean" truevalue="--discover-paths" falsevalue="" checked="false" label="Generates the initial set of paths" help="In the graph space an assembly 
                     is a collection of segment and edges/gaps between these segments. A path defines a potential walk through the segments and edges/gaps that corresponds to a hypothesis of the actual linear sequence" />
             </when>
         </conditional>
@@ -334,6 +338,19 @@
             </conditional>
             <output name="stats" value="test_11_stats.tabular" ftype="tabular"/>
         </test>
+        <!--Test 12 -->
+        <test expect_num_outputs="1">
+            <param name="input_file" value="dataset_04.gfa"/>
+            <conditional name="mode_condition">
+                <param name="selector" value="statistics"/>
+                <conditional name="statistics_condition">
+                    <param name="selector" value="assembly"/>
+                </conditional>
+                <param name="tabular" value="false"/>
+                <param name="discover_paths" value="true"/>
+            </conditional>
+            <output name="stats" value="test_12_stats.tabular" ftype="tabular"/>
+        </test>
     </tests>
     <help><![CDATA[