changeset 4:08d873cdd5f6 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44

--- a/macros.xml	Mon May 10 19:35:45 2021 +0000
+++ b/macros.xml	Wed Mar 20 13:17:36 2024 +0000
@@ -5,7 +5,11 @@
             <requirement type="package" version="@TOOL_VERSION@">obitools</requirement>
         </requirements>
     </xml>
-
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">obitools</xref>
+        </xrefs>
+    </xml>
     <token name="@TOOL_VERSION@">1.2.13</token>
     <token name="@PROFILE@">21.01</token>
 

--- a/obiclean.xml	Mon May 10 19:35:45 2021 +0000
+++ b/obiclean.xml	Wed Mar 20 13:17:36 2024 +0000
@@ -1,76 +1,77 @@
-<tool id="obi_clean" name="obiclean" version="@TOOL_VERSION@" profile="@PROFILE@">
-    <description>tags a set of sequences for PCR/sequencing errors identification</description>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
-    <expand macro="requirements"/>
-    <expand macro="stdio"/>
-
-    <command><![CDATA[
-        @GUNZIP_INPUT@
-        obiclean
-        --without-progress-bar
-        #if $distance
-            -d '$distance'
-        #end if
-        #if $key
-            -s '$key'
-        #end if
-        #if $ratio
-            -r '$ratio'
-        #end if
-        ${head}
-        @INPUT_FORMAT@
-        @OUT_FORMAT@
-        input 
-        @GZIP_OUTPUT@
-        >'$output'
-        @GENERATE_GALAXY_JSON@
-    ]]></command>
-    <inputs>
-        <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file" />
-        <param name="distance" type="integer" value="1" optional="true" label="Maximum numbers of differences between two variant sequences (default: 1)" />
-        <param name="key" type="text" optional="true" label="Specify an attribute containing sample definition" />
-        <param name="ratio" optional="true" type="float" value="1" label="Threshold ratio between counts (rare/abundant counts) of two sequence records so that the less abundant one is a variant of the more abundant (default: 1, i.e. all less abundant sequences are variants)" />
-        <param name="head" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Do you want to select only sequences with the head status in a least one sample?" />
-        <expand macro="input_format_options_macro"/>
-        <expand macro="out_format_macro"/>
-    </inputs>
-    <outputs>
-        <data format="auto" name="output"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="input" value="output_obiannotate.fasta" />
-            <param name="head" value="True"/>
-            <output name="output" file="output_obiclean_simple.fasta" ftype="fasta"/>
-        </test>
-        <test>
-            <param name="input" value="output_obiannotate.fasta.gz" />
-            <param name="key" value="merged_sample"/>
-            <param name="ratio" value="0.05"/>
-            <param name="head" value="False"/>
-            <output name="output" file="output_obiclean_advanced.fasta.gz" ftype="fasta.gz" decompress="true"/>
-        </test>
-    </tests>
-    <help><![CDATA[
-
-.. class:: infomark
-
-**What it does**
-
-obijoinpairedend aims at joining the two reads of a paired-end library.
-
-For this purpose, it concatenates sequence merging the forward read and the reversed-complemented reverse read.
-
-The program uses as input one or two sequences reads files.
-
-If two files are used one of them must be specified using the -r option. Sequence records corresponding to the same read pair must be in the same order in the two files.
-If just one file is provided, sequence records are supposed to be all of the same length. The first half of the sequence is used as forward read, the second half is used as the reverse read.
-
-@OBITOOLS_LINK@
-
-        ]]>
-    </help>
-    <expand macro="citation" />
-    </tool>
+<tool id="obi_clean" name="obiclean" version="@TOOL_VERSION@" profile="@PROFILE@">
+    <description>tags a set of sequences for PCR/sequencing errors identification</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+
+    <command><![CDATA[
+        @GUNZIP_INPUT@
+        obiclean
+        --without-progress-bar
+        #if $distance
+            -d '$distance'
+        #end if
+        #if $key
+            -s '$key'
+        #end if
+        #if $ratio
+            -r '$ratio'
+        #end if
+        ${head}
+        @INPUT_FORMAT@
+        @OUT_FORMAT@
+        input 
+        @GZIP_OUTPUT@
+        >'$output'
+        @GENERATE_GALAXY_JSON@
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file"/>
+        <param name="distance" type="integer" value="1" optional="true" label="Maximum numbers of differences between two variant sequences (default: 1)"/>
+        <param name="key" type="text" optional="true" label="Specify an attribute containing sample definition"/>
+        <param name="ratio" optional="true" type="float" value="1" label="Threshold ratio between counts (rare/abundant counts) of two sequence records so that the less abundant one is a variant of the more abundant (default: 1, i.e. all less abundant sequences are variants)"/>
+        <param name="head" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Do you want to select only sequences with the head status in a least one sample?"/>
+        <expand macro="input_format_options_macro"/>
+        <expand macro="out_format_macro"/>
+    </inputs>
+    <outputs>
+        <data format="auto" name="output"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input" value="output_obiannotate.fasta" />
+            <param name="head" value="True"/>
+            <output name="output" file="output_obiclean_simple.fasta" ftype="fasta"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="output_obiannotate.fasta.gz" />
+            <param name="key" value="merged_sample"/>
+            <param name="ratio" value="0.05"/>
+            <param name="head" value="False"/>
+            <output name="output" file="output_obiclean_advanced.fasta.gz" ftype="fasta.gz" decompress="true"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What it does**
+
+obijoinpairedend aims at joining the two reads of a paired-end library.
+
+For this purpose, it concatenates sequence merging the forward read and the reversed-complemented reverse read.
+
+The program uses as input one or two sequences reads files.
+
+If two files are used one of them must be specified using the -r option. Sequence records corresponding to the same read pair must be in the same order in the two files.
+If just one file is provided, sequence records are supposed to be all of the same length. The first half of the sequence is used as forward read, the second half is used as the reverse read.
+
+@OBITOOLS_LINK@
+
+        ]]>
+    </help>
+    <expand macro="citation"/>
+    </tool>

--- a/test-data/input_ngsfilter_extrafile.txt	Mon May 10 19:35:45 2021 +0000
+++ b/test-data/input_ngsfilter_extrafile.txt	Wed Mar 20 13:17:36 2024 +0000
@@ -1,4 +1,4 @@
-wolf_diet    13a_F730603      aattaac  TTAGATACCCCACTATGC    TAGAACAGGCTCCTCTAG     F       @
-wolf_diet    15a_F730814      gaagtag  TTAGATACCCCACTATGC    TAGAACAGGCTCCTCTAG     F       @
-wolf_diet    26a_F040644      gaatatc  TTAGATACCCCACTATGC    TAGAACAGGCTCCTCTAG     F       @
-wolf_diet    29a_F260619      gcctcct  TTAGATACCCCACTATGC    TAGAACAGGCTCCTCTAG     F       @
+wolf_diet	13a_F730603	aattaac	TTAGATACCCCACTATGC	TAGAACAGGCTCCTCTAG	F	@
+wolf_diet	15a_F730814	gaagtag	TTAGATACCCCACTATGC	TAGAACAGGCTCCTCTAG	F	@
+wolf_diet	26a_F040644	gaatatc	TTAGATACCCCACTATGC	TAGAACAGGCTCCTCTAG	F	@
+wolf_diet	29a_F260619	gcctcct	TTAGATACCCCACTATGC	TAGAACAGGCTCCTCTAG	F	@