changeset 5:a829941376bd draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45

--- a/illuminapairedend.xml	Wed Mar 20 13:17:09 2024 +0000
+++ b/illuminapairedend.xml	Thu Oct 30 16:05:55 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="obi_illumina_pairend" name="Illuminapairedend" version="@TOOL_VERSION@" profile="@PROFILE@">
+<tool id="obi_illumina_pairend" name="Illuminapairedend" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>Construct consensus reads from Illumina pair-end reads</description>
     <macros>
         <import>macros.xml</import>
@@ -8,20 +8,20 @@
     <expand macro="stdio"/>
     <command>
         <![CDATA[
-        #if $inputfastq3p.ext.endswith(".gz")
-            gunzip -c '$inputfastq3p' > fastq3p.fastq &&
-            gunzip -c '$inputfastq5p' > fastq5p.fastq &&
+        #if $inputfastq.forward.ext.endswith(".gz")
+            gunzip -c '$inputfastq.forward' > fastq3p.fastq &&
+            gunzip -c '$inputfastq.reverse' > fastq5p.fastq &&
         #else
-            ln -s '$inputfastq3p' fastq3p.fastq &&
-            ln -s '$inputfastq5p' fastq5p.fastq &&
+            ln -s '$inputfastq.forward' fastq3p.fastq &&
+            ln -s '$inputfastq.reverse' fastq5p.fastq &&
         #end if
 
         illuminapairedend
         ##--index-file=
-        #if $inputfastq3p.ext.startswith("fastqsolexa")
+        #if $inputfastq.forward.ext.startswith("fastqsolexa")
             ##input file is in fastq nucleic format produced by solexa sequencer
             --solexa
-        #else if $inputfastq3p.ext.startswith("fastqillumina")
+        #else if $inputfastq.forward.ext.startswith("fastqillumina")
             ##input file is in fastq nucleic format produced by solexa sequencer
             --illumina
         #else
@@ -30,37 +30,44 @@
         #end if
         --without-progress-bar
         --score-min='$score'
-        -r fastq3p.fastq 
+        -r fastq3p.fastq
         fastq5p.fastq
-        #if $inputfastq3p.ext.endswith(".gz")
-            | gzip -c 
+        #if $inputfastq.forward.ext.endswith(".gz")
+            | gzip -c
         #end if
         > '$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="inputfastq" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" type="data_collection" collection_type="paired" label="Paired reads" help="file of 3p and 5p 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" />
+        <data name="output" format_source="inputfastq"/>
     </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="inputfastq">
+                    <collection type="paired">
+                        <element name="forward" value="wolf_small.F.fastq" ftype="fastqsanger"/>
+                        <element name="reverse" value="wolf_small.R.fastq" ftype="fastqsanger"/>
+                    </collection>
+            </param>
            <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="inputfastq">
+                    <collection type="paired">
+                        <element name="forward" value="wolf_small.F.fastq.gz" ftype="fastqsanger.gz"/>
+                        <element name="reverse" value="wolf_small.R.fastq.gz" ftype="fastqsanger.gz"/>
+                    </collection>
+            </param>
            <param name="score" value="40.0" />
            <output name="output" file="illuminapairedend.output.fastq.gz" ftype="fastqsanger.gz" decompress="true"/>
        </test>
-   </tests>
+    </tests>
 
     <help><![CDATA[
 
@@ -80,12 +87,9 @@
 \* 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.
+The program uses as input a pair of fastq sequences read datasets.
 
-\* 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.
+illuminapairedend aligns the forward sequence record with the reverse complement of the reverse sequence record. The alignment algorithm takes into account the base qualities.
 
 @OBITOOLS_LINK@
 
@@ -95,3 +99,6 @@
 
 </tool>
 
+
+
+