diff gfastats.xml @ 1:2b8b4cacb83d draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"

--- a/gfastats.xml	Wed Mar 09 10:29:20 2022 +0000
+++ b/gfastats.xml	Mon Apr 25 09:38:18 2022 +0000
@@ -30,7 +30,9 @@
             #if $mode_condition.sort
                 --sort $mode_condition.sort
             #end if
-            $mode_condition.homopolymer_compress
+            #if $mode_condition.homopolymer_compress
+                --homopolymer-compress $mode_condition.homopolymer_compress
+            #end if
             -o dataset.$mode_condition.output_condition.out_format
             #if $mode_condition.output_condition.out_format == 'fasta'
                 #if $mode_condition.output_condition.line_length
@@ -41,7 +43,7 @@
                     --line-length $mode_condition.output_condition.line_length
                 #end if
             #end if
-        #else
+        #else if $mode_condition.selector == "statistics"
             #if $mode_condition.statistics_condition.selector == 'size'
                 --out-size $mode_condition.statistics_condition.out_size
             #else if $mode_condition.statistics_condition.selector == 'coordinates'
@@ -52,9 +54,13 @@
                 --seq-report
                 $mode_condition.statistics_condition.out_sequence
             #end if
-            $mode_condition.tabular > '$stats' 
+            $mode_condition.tabular > '$stats'
+        #else
+            --agp-to-path $mode_condition.agp_to_path
+            $mode_condition.discover_paths
+            -o dataset.gfa
         #end if
-        #if $mode_condition.selector == 'manipulation'
+        #if $mode_condition.selector == 'manipulation' or $mode_condition.selector == 'scaffolding'
             && mv dataset* output_dataset
         #end if
     ]]></command>
@@ -95,6 +101,7 @@
             <param name="selector" type="select" label="Tool mode">
                 <option value="statistics">Summary statistics generation</option>
                 <option value="manipulation">Genome assembly manipulation</option>
+                <option value="scaffolding">Scaffolding</option>
             </param>
             <when value="manipulation">
                 <param argument="--swiss-army-knife" type="data"
@@ -128,8 +135,7 @@
                     <option value="largest">Largest</option>
                     <option value="smallest">Smallest</option>
                 </param>
-                <param argument="--homopolymer-compress" type="boolean" truevalue="--homopolymer-compress" falsevalue="" checked="false"
-                    label="Homopolymer compression" help="Compress all the homopolymers in the input"/>
+                <param argument="--homopolymer-compress" type="integer" min="0" value="" optional="true" label="Homopolymer compression" help="Compress all the homopolymers in the input above the given threshhold" />
             </when>
             <when value="statistics">
                 <conditional name="statistics_condition">
@@ -167,6 +173,11 @@
                 <param argument="--tabular" type="boolean" truevalue="--tabular" falsevalue="" checked="true"
                     label="Tabular-format output" help="Generate output in tabular format"/>
             </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 
+                    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>
     </inputs>
     <outputs>
@@ -177,7 +188,7 @@
             </change_format>
         </data>
         <data name="output" format="fastq" from_work_dir="output_dataset" label="${tool.name} on ${on_string}: edited sequences">
-            <filter>mode_condition['selector'] == 'manipulation'</filter>
+            <filter>mode_condition['selector'] == 'manipulation' or mode_condition['selector'] == 'scaffolding'</filter>
             <change_format>
                 <when input="mode_condition.output_condition.out_format" value="fasta" format="fasta"/>
                 <when input="mode_condition.output_condition.out_format" value="fasta.gz" format="fasta.gz"/>
@@ -185,6 +196,7 @@
                 <when input="mode_condition.output_condition.out_format" value="fastq.gz" format="fastq.gz"/>
                 <when input="mode_condition.output_condition.out_format" value="gfa" format="gfa1"/>
                 <when input="mode_condition.output_condition.out_format" value="gfa.gz" format="gfa1.gz"/>
+                <when input="mode_condition.selector" value="scaffolding" format="gfa1"/>
             </change_format>
         </data>
     </outputs>
@@ -288,10 +300,31 @@
                     <param name="out_format" value="fasta.gz"/>
                 </conditional>
                 <param name="sort" value="ascending"/>
-                <param name="homopolymer_compress" value="true"/>
             </conditional>
             <output name="output" value="test_08.fasta.gz" ftype="fasta.gz"/>
         </test>
+        <!--Test 09 -->
+        <test expect_num_outputs="1">
+            <param name="input_file" value="dataset_03.fasta"/>
+            <conditional name="mode_condition">
+                <param name="selector" value="manipulation"/>
+                <conditional name="output_condition">
+                    <param name="out_format" value="fasta.gz"/>
+                </conditional>
+                <param name="homopolymer_compress" value="10"/>
+            </conditional>
+            <output name="output" value="test_09.fasta.gz" ftype="fasta.gz"/>
+        </test>
+        <!--Test 10 -->
+        <test expect_num_outputs="1">
+            <param name="input_file" value="dataset_04.gfa"/>
+            <conditional name="mode_condition">
+                <param name="selector" value="scaffolding"/>
+                <param name="agp_to_path" value="dataset_05.agp"/>
+                <param name="discover_paths" value="true"/>
+            </conditional>
+            <output name="output" value="test_10.gfa" ftype="gfa1"/>
+        </test>
     </tests>
     <help><![CDATA[