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changeset 7:3ef480892a9f draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
author bgruening
date Fri, 23 Dec 2022 20:00:51 +0000
parents 690c2caa367e
children 6ec1b853c8fd
files gfastats.xml macros.xml test-data/swiss_army.sak test-data/test_01.fasta.gz
diffstat 4 files changed, 51 insertions(+), 23 deletions(-) [+]
line wrap: on
line diff
--- a/gfastats.xml	Mon Dec 05 12:20:31 2022 +0000
+++ b/gfastats.xml	Fri Dec 23 20:00:51 2022 +0000
@@ -35,13 +35,14 @@
             #end if
             $mode_condition.discover_paths
             -o dataset.$mode_condition.output_condition.out_format
-            #if $mode_condition.output_condition.out_format == 'fasta'
+            #if $mode_condition.output_condition.out_format in ['fasta','fasta.gz']
                 #if $mode_condition.output_condition.line_length
                     --line-length $mode_condition.output_condition.line_length
                 #end if
-            #else if $mode_condition.output_condition.out_format == 'fasta.gz'
-                #if $mode_condition.output_condition.line_length
-                    --line-length $mode_condition.output_condition.line_length
+            #end if
+            #if $mode_condition.output_condition.out_format in ['gfa','gfa.gz']
+                #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
             #end if
         #else if $mode_condition.selector == "statistics"
@@ -55,6 +56,7 @@
                 --seq-report
                 $mode_condition.statistics_condition.out_sequence
             #end if
+            $mode_condition.locale
             $mode_condition.discover_paths
             $mode_condition.tabular > '$stats'
         #else
@@ -93,10 +95,10 @@
                 <param argument="--include-bed" type="data" optional="true"
                     format="bed" label="Include specific intervals"
                     help="Generates output on a subset list of headers or coordinates   
-                        in 0-based bed format. It can be combined with --exclude-bed. Optional"/>
+                        in 0-based bed format. It can be combined with --exclude-bed. Optional."/>
                 <param argument="--exclude-bed" type="data" format="bed" optional="true"
                     label="Exclude specific intervals"
-                    help="Exclude a subset of headers or coordinates in 0-base bed format. It can be conmbined with --include-bed Optional"/>
+                    help="Exclude a subset of headers or coordinates in 0-base bed format. It can be conmbined with --include-bed. Optional."/>
             </when>
             <when value="false"/>
         </conditional>
@@ -128,19 +130,23 @@
                     </when>
                     <when value="fastq"/>
                     <when value="fastq.gz"/>
-                    <when value="gfa"/>
-                    <when value="gfa.gz"/>
-		</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 
-                    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" />
-                <param argument="--sort" type="select" label="Sort sequences" help="Specify how to sort the sequences. Ascending/descending used the sequence/path header.">
+                    <when value="gfa">
+                        <expand macro="terminal_overlaps_macro"/>
+                    </when>
+                    <when value="gfa.gz">
+                        <expand macro="terminal_overlaps_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 
+                    is a collection of segments 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." />
+                <param argument="--sort" type="select" label="Sort sequences" help="Specify how to sort the sequences. Ascending/descending uses the sequence/path header.">
                     <option value="" selected="true">Disabled</option>
                     <option value="ascending">Ascending</option>
                     <option value="descending">Descending</option>
                     <option value="largest">Largest</option>
                     <option value="smallest">Smallest</option>
                 </param>
-                <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" />
+                <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">
                 <conditional name="statistics_condition">
@@ -175,6 +181,8 @@
                             label="Report actual sequence" help="It reports also the actual sequence"/>
                     </when>
                 </conditional>
+                <param argument="--locale" type="boolean" truevalue="--locale en_US.UTF-8" falsevalue="" checked="true"
+                    label="Thousands separator in output" help="Use commas for thousands separator in output?"/>
                 <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 
@@ -211,10 +219,6 @@
         <!--Test 01 -->
         <test expect_num_outputs="1">
             <param name="input_file" value="dataset_01.fastq.gz"/>
-            <conditional name="target_condition">
-                <param name="target_condition" value="true"/>
-                <param name="target_sequence" value="S1_1"/>
-            </conditional>
             <conditional name="mode_condition">
                 <param name="selector" value="manipulation"/>
                 <param name="swiss_army_knife" value="swiss_army.sak"/>
@@ -237,10 +241,11 @@
                     <param name="selector" value="size"/>
                     <param name="out_size" value="c"/>
                 </conditional>
+                <param name="locale" value="false"/>
             </conditional>
             <output name="stats" ftype="tabular">
                 <assert_contents>
-                    <has_text text="S1_76.1&#009;9445" />
+                    <has_text text="S1_1.1&#009;8550" />
                 </assert_contents>
             </output>
         </test>
@@ -252,6 +257,7 @@
                 <conditional name="statistics_condition">
                     <param name="selector" value="sequence"/>
                 </conditional>
+                <param name="locale" value="false"/>
             </conditional>
             <output name="stats" ftype="tabular">
                 <assert_contents>
@@ -268,6 +274,7 @@
                     <param name="selector" value="assembly"/>
                     <param name="expected_genomesize" value="600000"/>
                 </conditional>
+                <param name="locale" value="false"/>
             </conditional>
             <output name="stats" value="test_04_stats.tabular" ftype="tabular"/>
         </test>
@@ -280,6 +287,7 @@
                     <param name="selector" value="coordinates"/>
                     <param name="out_coord" value="a"/>
                 </conditional>
+                <param name="locale" value="false"/>
             </conditional>
             <output name="stats" value="test_05_stats.tabular" ftype="tabular"/>
         </test>
@@ -302,6 +310,7 @@
                 <conditional name="statistics_condition">
                     <param name="selector" value="assembly"/>
                 </conditional>
+                <param name="locale" value="false"/>
                 <param name="tabular" value="false"/>
             </conditional>
             <output name="stats" value="test_07_stats.tabular" ftype="tabular"/>
@@ -347,6 +356,9 @@
                 <param name="target_option" value="true"/>
                 <param name="include_bed" value="regions.bed"/>
             </conditional>
+            <conditional name="mode_condition">
+                <param name="locale" value="false"/>
+            </conditional>
             <output name="stats" value="test_11_stats.tabular" ftype="tabular"/>
         </test>
         <!--Test 12 -->
@@ -357,6 +369,7 @@
                 <conditional name="statistics_condition">
                     <param name="selector" value="assembly"/>
                 </conditional>
+                <param name="locale" value="false"/>
                 <param name="tabular" value="false"/>
                 <param name="discover_paths" value="true"/>
             </conditional>
--- a/macros.xml	Mon Dec 05 12:20:31 2022 +0000
+++ b/macros.xml	Fri Dec 23 20:00:51 2022 +0000
@@ -1,6 +1,6 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.3.5</token>
-    <token name="@SUFFIX_VERSION@">2</token>
+    <token name="@TOOL_VERSION@">1.3.6</token>
+    <token name="@SUFFIX_VERSION@">0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">gfastats</requirement>
@@ -26,7 +26,22 @@
     </xml>
     <xml name="length_macro">
         <param argument="--line-length" type="integer" min="0" max="80" value=""
-            optional="true" label="Especify line length"
-            help="Specifies line length when output format is fasta. Default has no line breaks."/>
+            optional="true" label="Specify line length"
+            help="Optional: specifies line length when output format is fasta. Default has no line breaks."/>
+    </xml>
+    <xml name="terminal_overlaps_macro">
+        <conditional name="terminal_overlaps_condition">
+            <param name="terminal_overlaps_select" type="select" 
+                label="Terminal overlaps selection" help="Optional: Do you want to detect terminal overlaps?">
+                <option value="no">No (default)</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no"/>
+            <when value="yes">
+                <param name="terminal_overlaps_length" type="integer" min="500" value="500" 
+                optional="false" label="Terminal overlaps length" 
+                help="Integer for minimum length required to count as an overlap for detecting terminal overlaps (minimum is 500)" />
+            </when>
+        </conditional>
     </xml>
 </macros>
--- a/test-data/swiss_army.sak	Mon Dec 05 12:20:31 2022 +0000
+++ b/test-data/swiss_army.sak	Fri Dec 23 20:00:51 2022 +0000
@@ -1,1 +1,1 @@
-REMOVE	s1_1
+REMOVE	S1_1.1
Binary file test-data/test_01.fasta.gz has changed