diff gfastats.xml @ 8:6ec1b853c8fd draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 53b8f235e87107323cc6e636cc0d069551a44dec

--- a/gfastats.xml	Fri Dec 23 20:00:51 2022 +0000
+++ b/gfastats.xml	Thu Oct 10 09:58:15 2024 +0000
@@ -1,10 +1,10 @@
-<tool id="gfastats" name="gfastats" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="20.01">
-    <description>the swiss army knife for genome assembly</description>
+<tool id="gfastats" name="gfastats" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2">
+    <description>The swiss army knife for Genome Assembly</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements" />
     <expand macro="biotools"/>
+    <expand macro="requirements"/>
     <version_command>gfastats --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
         gfastats
@@ -34,6 +34,7 @@
                 --homopolymer-compress $mode_condition.homopolymer_compress
             #end if
             $mode_condition.discover_paths
+            $mode_condition.remove_terminal_gaps
             -o dataset.$mode_condition.output_condition.out_format
             #if $mode_condition.output_condition.out_format in ['fasta','fasta.gz']
                 #if $mode_condition.output_condition.line_length
@@ -53,7 +54,7 @@
             #else if $mode_condition.statistics_condition.selector == 'assembly'
                 --nstar-report
             #else
-                --seq-report
+                --segment-report
                 $mode_condition.statistics_condition.out_sequence
             #end if
             $mode_condition.locale
@@ -146,6 +147,7 @@
                     <option value="largest">Largest</option>
                     <option value="smallest">Smallest</option>
                 </param>
+                <param argument="--remove-terminal-gaps" type="boolean" truevalue="--remove-terminal-gaps" falsevalue="" checked="false" label="Remove gaps from the beginning and end of sequences"/>
                 <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 threshold." />
             </when>
             <when value="statistics">
@@ -154,7 +156,7 @@
                         <option value="assembly" selected="true">Genome assembly statistics (--nstar-report)</option>
                         <option value="size">Scaffold, contig or gap sizes (--out-size)</option>
                         <option value="coordinates">AGP, contig or gap coordinates (--out-coord)</option>
-                        <option value="sequence">Sequence statistics (--seq-report)</option>
+                        <option value="sequence">Sequence statistics (--segment-report)</option>
                     </param>
                     <when value="size">
                         <param argument="--out-size" type="select" label="Feature for reporting sizes"
@@ -228,6 +230,19 @@
             </conditional>
             <output name="output" value="test_01.fasta.gz" ftype="fasta.gz"/>
         </test>
+        <!--Test 01 A) -->
+        <test expect_num_outputs="1">
+            <param name="input_file" value="dataset_01.fastq.gz"/>
+            <conditional name="mode_condition">
+                <param name="selector" value="manipulation"/>
+                <param name="swiss_army_knife" value="swiss_army.sak"/>
+                <param name="remove_terminal_gaps" value="true"/>
+                <conditional name="output_condition">
+                    <param name="out_format" value="fasta.gz"/>
+                </conditional>
+            </conditional>
+            <output name="output" value="test_01_a.fasta.gz" ftype="fasta.gz"/>
+        </test>
         <!--Test 02 -->
         <test expect_num_outputs="1">
             <param name="input_file" value="dataset_01.fastq.gz"/>
@@ -418,5 +433,5 @@
 gfastats allows extensive assembly manipulation at the sequence level. Manipulation is achieved using a set of instructions provided as an ordered list in a file to the option **swiss army knife**. See the `instruction wiki <https://github.com/vgl-hub/gfastats/tree/main/instructions>`_ for a full list of instructions.
 
   ]]></help>
-    <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>