# HG changeset patch
# User iuc
# Date 1710940629 0
# Node ID 8cb6bd5118794c2429bddd77c3cf7a75b6212eba
# Parent  83fbdf93d51ec250f9e97ecfe4eb2f426b14ca5b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44

diff -r 83fbdf93d51e -r 8cb6bd511879 illuminapairedend.xml
--- a/illuminapairedend.xml	Mon May 10 19:36:09 2021 +0000
+++ b/illuminapairedend.xml	Wed Mar 20 13:17:09 2024 +0000
@@ -1,95 +1,97 @@
-<tool id="obi_illumina_pairend" name="Illuminapairedend" version="@TOOL_VERSION@" profile="@PROFILE@">
-    <description>Construct consensus reads from Illumina pair-end reads</description>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
-    <expand macro="requirements"/>
-    <expand macro="stdio"/>
-    <command>
-        <![CDATA[
-        #if $inputfastq3p.ext.endswith(".gz")
-            gunzip -c '$inputfastq3p' > fastq3p.fastq &&
-            gunzip -c '$inputfastq5p' > fastq5p.fastq &&
-        #else
-            ln -s '$inputfastq3p' fastq3p.fastq &&
-            ln -s '$inputfastq5p' fastq5p.fastq &&
-        #end if
-
-        illuminapairedend
-        ##--index-file=
-        #if $inputfastq3p.ext.startswith("fastqsolexa")
-            ##input file is in fastq nucleic format produced by solexa sequencer
-            --solexa
-        #else if $inputfastq3p.ext.startswith("fastqillumina")
-            ##input file is in fastq nucleic format produced by solexa sequencer
-            --illumina
-        #else
-            ## input file is in sanger fastq nucleic format (standard fastq)
-            --sanger
-        #end if
-        --without-progress-bar
-        --score-min='$score'
-        -r fastq3p.fastq 
-        fastq5p.fastq
-        #if $inputfastq3p.ext.endswith(".gz")
-            | gzip -c 
-        #end if
-        > '$output'
-        ]]>
-    </command>
-    <inputs>
-        <param name="inputfastq3p" type="data" format="fastq,fastq.gz" label="Read from file" help="file of 3p (1:) Illumina pair-end reads to assemble in sanger fastq nucleic format (standard fastq)" />
-        <param name="inputfastq5p" type="data" format="fastq,fastq.gz" label="Read from file" help="file of 5p (2:) Illumina pair-end reads to assemble in sanger fastq nucleic format (standard fastq)" />
-        <param name="score" type="float" value="40.0" label="minimum score for keeping aligment"/>
-    </inputs>
-    <outputs>
-        <data name="output" format_source="inputfastq3p" label="${tool.name} on ${on_string}: assembly results" />
-    </outputs>
-
-    <tests>
-       <test>
-           <param name="inputfastq3p" value="wolf_small.F.fastq" ftype="fastqsanger" />
-           <param name="inputfastq5p" value="wolf_small.R.fastq" ftype="fastqsanger" />
-           <param name="score" value="40.0" />
-           <output name="output" file="illuminapairedend.output.fastq" ftype="fastqsanger" />
-       </test>
-       <test>
-           <param name="inputfastq3p" value="wolf_small.F.fastq.gz" ftype="fastqsanger.gz" />
-           <param name="inputfastq5p" value="wolf_small.R.fastq.gz" ftype="fastqsanger.gz" />
-           <param name="score" value="40.0" />
-           <output name="output" file="illuminapairedend.output.fastq.gz" ftype="fastqsanger.gz" decompress="true"/>
-       </test>
-   </tests>
-
-    <help><![CDATA[
-
-.. class:: warning
-
-**Warning:**
-Sequence records corresponding to the same read pair must be in the same order in the two files
-
---------
-
-.. class:: infomark
-
-**What it does**
-
-illuminapairedend aims at aligning the two reads of a pair-end library sequenced using an Illumina platform :
-
-\* If the two reads overlap, it returns the consensus sequence together with its quality
-\* Otherwise, it concatenates sequence merging the forward read and the reversed-complemented reverse read.
-
-The program uses as input one or two fastq 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 th  e sequence is used as forward read, the second half is used as the reverse read.
-
-illuminapairedend align the forward sequence record with the reverse complement of the reverse sequence record. The alignment algorithm takes into account the base qualities.
-
-@OBITOOLS_LINK@
-
-]]>
-    </help>
-    <expand macro="citation" />
-
-</tool>
+<tool id="obi_illumina_pairend" name="Illuminapairedend" version="@TOOL_VERSION@" profile="@PROFILE@">
+    <description>Construct consensus reads from Illumina pair-end reads</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command>
+        <![CDATA[
+        #if $inputfastq3p.ext.endswith(".gz")
+            gunzip -c '$inputfastq3p' > fastq3p.fastq &&
+            gunzip -c '$inputfastq5p' > fastq5p.fastq &&
+        #else
+            ln -s '$inputfastq3p' fastq3p.fastq &&
+            ln -s '$inputfastq5p' fastq5p.fastq &&
+        #end if
+
+        illuminapairedend
+        ##--index-file=
+        #if $inputfastq3p.ext.startswith("fastqsolexa")
+            ##input file is in fastq nucleic format produced by solexa sequencer
+            --solexa
+        #else if $inputfastq3p.ext.startswith("fastqillumina")
+            ##input file is in fastq nucleic format produced by solexa sequencer
+            --illumina
+        #else
+            ## input file is in sanger fastq nucleic format (standard fastq)
+            --sanger
+        #end if
+        --without-progress-bar
+        --score-min='$score'
+        -r fastq3p.fastq 
+        fastq5p.fastq
+        #if $inputfastq3p.ext.endswith(".gz")
+            | gzip -c 
+        #end if
+        > '$output'
+        ]]>
+    </command>
+    <inputs>
+        <param name="inputfastq3p" type="data" format="fastq,fastq.gz" label="Read from file" help="file of 3p (1:) Illumina pair-end reads to assemble in sanger fastq nucleic format (standard fastq)" />
+        <param name="inputfastq5p" type="data" format="fastq,fastq.gz" label="Read from file" help="file of 5p (2:) Illumina pair-end reads to assemble in sanger fastq nucleic format (standard fastq)" />
+        <param name="score" type="float" value="40.0" label="minimum score for keeping aligment"/>
+    </inputs>
+    <outputs>
+        <data name="output" format_source="inputfastq3p" label="${tool.name} on ${on_string}: assembly results" />
+    </outputs>
+
+    <tests>
+       <test expect_num_outputs="1">
+           <param name="inputfastq3p" value="wolf_small.F.fastq" ftype="fastqsanger" />
+           <param name="inputfastq5p" value="wolf_small.R.fastq" ftype="fastqsanger" />
+           <param name="score" value="40.0" />
+           <output name="output" file="illuminapairedend.output.fastq" ftype="fastqsanger" />
+       </test>
+       <test expect_num_outputs="1">
+           <param name="inputfastq3p" value="wolf_small.F.fastq.gz" ftype="fastqsanger.gz" />
+           <param name="inputfastq5p" value="wolf_small.R.fastq.gz" ftype="fastqsanger.gz" />
+           <param name="score" value="40.0" />
+           <output name="output" file="illuminapairedend.output.fastq.gz" ftype="fastqsanger.gz" decompress="true"/>
+       </test>
+   </tests>
+
+    <help><![CDATA[
+
+.. class:: warning
+
+**Warning:**
+Sequence records corresponding to the same read pair must be in the same order in the two files
+
+--------
+
+.. class:: infomark
+
+**What it does**
+
+illuminapairedend aims at aligning the two reads of a pair-end library sequenced using an Illumina platform :
+
+\* If the two reads overlap, it returns the consensus sequence together with its quality
+\* Otherwise, it concatenates sequence merging the forward read and the reversed-complemented reverse read.
+
+The program uses as input one or two fastq 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 th  e sequence is used as forward read, the second half is used as the reverse read.
+
+illuminapairedend align the forward sequence record with the reverse complement of the reverse sequence record. The alignment algorithm takes into account the base qualities.
+
+@OBITOOLS_LINK@
+
+]]>
+    </help>
+    <expand macro="citation" />
+
+</tool>
+
diff -r 83fbdf93d51e -r 8cb6bd511879 macros.xml
--- a/macros.xml	Mon May 10 19:36:09 2021 +0000
+++ b/macros.xml	Wed Mar 20 13:17:09 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>
 
diff -r 83fbdf93d51e -r 8cb6bd511879 test-data/input_ngsfilter_extrafile.txt
--- a/test-data/input_ngsfilter_extrafile.txt	Mon May 10 19:36:09 2021 +0000
+++ b/test-data/input_ngsfilter_extrafile.txt	Wed Mar 20 13:17:09 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	@