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changeset 11:7729cd89aaf7 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 9286bd08068c6dae43192d1a19e898aa0a75452c
author bgruening
date Wed, 05 Feb 2025 10:45:26 +0000
parents 764f2516d837
children 0393c0415171
files gfastats.xml macros.xml test-data/test_13.gfa test-data/test_14.gfa
diffstat 4 files changed, 45 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/gfastats.xml	Thu Dec 12 20:37:13 2024 +0000
+++ b/gfastats.xml	Wed Feb 05 10:45:26 2025 +0000
@@ -42,6 +42,7 @@
                 #end if
             #end if
             #if $mode_condition.output_condition.out_format in ['gfa','gfa.gz']
+                $mode_condition.output_condition.no_sequence
                 #if $mode_condition.output_condition.terminal_overlaps_condition.terminal_overlaps_select == 'yes':
                 --discover-terminal-overlaps $mode_condition.output_condition.terminal_overlaps_condition.terminal_overlaps_length
                 #end if
@@ -63,6 +64,7 @@
         #else
             --agp-to-path $mode_condition.agp_to_path
             $mode_condition.discover_paths
+            $mode_condition.no_sequence
             -o dataset.gfa
         #end if
         --threads \${GALAXY_SLOTS:-8}
@@ -133,9 +135,11 @@
                     <when value="fastq.gz"/>
                     <when value="gfa">
                         <expand macro="terminal_overlaps_macro"/>
+                        <expand macro="no_sequence_macro"/>
                     </when>
                     <when value="gfa.gz">
                         <expand macro="terminal_overlaps_macro"/>
+                        <expand macro="no_sequence_macro"/>
                     </when>
 		        </conditional>
                 <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 
@@ -194,6 +198,7 @@
                 <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" />
+                <expand macro="no_sequence_macro"/>
             </when>
         </conditional>
     </inputs>
@@ -390,6 +395,30 @@
             </conditional>
             <output name="stats" value="test_12_stats.tabular" ftype="tabular"/>
         </test>
+        <!--Test 13 -->
+        <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"/>
+                <param name="no_sequence" value="true"/>
+            </conditional>
+            <output name="output" value="test_13.gfa" ftype="gfa1"/>
+        </test>
+        <!--Test 14 -->
+        <test expect_num_outputs="1">
+            <param name="input_file" value="dataset_01_a.fasta.gz"/>
+            <conditional name="mode_condition">
+                <param name="selector" value="manipulation"/>
+                <conditional name="output_condition">
+                    <param name="out_format" value="gfa"/>
+                    <param name="no_sequence" value="true"/>
+                </conditional>
+            <param name="sort" value="ascending"/>
+            </conditional>
+            <output name="output" value="test_14.gfa" ftype="gfa1"/>
+        </test>
     </tests>
     <help><![CDATA[
 
--- a/macros.xml	Thu Dec 12 20:37:13 2024 +0000
+++ b/macros.xml	Wed Feb 05 10:45:26 2025 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.3.9</token>
-    <token name="@SUFFIX_VERSION@">1</token>
+    <token name="@SUFFIX_VERSION@">2</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">gfastats</requirement>
@@ -44,4 +44,7 @@
             </when>
         </conditional>
     </xml>
+    <xml name="no_sequence_macro">
+        <param argument="--no-sequence" type="boolean" truevalue="--no-sequence" falsevalue="" checked="false" label="Do not include sequences in the GFA output" help="Select Yes for a lighter GFA file."/>
+    </xml>
 </macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_13.gfa	Wed Feb 05 10:45:26 2025 +0000
@@ -0,0 +1,2 @@
+H	VN:Z:1.2
+S	edge_1	*	LN:i:419576	dp:i:14
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_14.gfa	Wed Feb 05 10:45:26 2025 +0000
@@ -0,0 +1,10 @@
+H	VN:Z:1.2
+S	seq_00001~59..230276.2	*	LN:i:5006
+S	seq_00001~59..230276.4	*	LN:i:996
+S	seq_00001~59..230276.6	*	LN:i:634
+S	seq_00001~59..230276.8	*	LN:i:5185
+J	seq_00001~59..230276.2	+	seq_00001~59..230276.2	+	62
+J	seq_00001~59..230276.2	+	seq_00001~59..230276.4	+	13
+J	seq_00001~59..230276.4	+	seq_00001~59..230276.6	+	25
+J	seq_00001~59..230276.6	+	seq_00001~59..230276.8	+	19
+P	seq_00001~59..230276	;seq_00001~59..230276.2+;seq_00001~59..230276.4+;seq_00001~59..230276.6+;seq_00001~59..230276.8+	*