diff hicup_macros.xml @ 5:396e8c4ebfee draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef

--- a/hicup_macros.xml	Fri May 25 17:48:10 2018 -0400
+++ b/hicup_macros.xml	Sat Oct 22 08:43:54 2022 +0000
@@ -1,11 +1,10 @@
 <macros>
-    <token name="@VERSION@">0.6.1</token>
+    <token name="@VERSION@">0.8.3</token>
     <xml name="requirements_hicup">
         <requirements>
             <requirement type="package" version="@VERSION@">hicup</requirement>
-            <requirement type="package" version="2.2.6">bowtie2</requirement>
-            <requirement type="package" version="1.2">samtools</requirement>
-            <requirement type="package" version="0.13.1">docutils</requirement>
+            <requirement type="package" version="2.4.5">bowtie2</requirement>
+            <requirement type="package" version="1.16.1">samtools</requirement>
             <yield/>
         </requirements>
         <version_command>hicup --version</version_command>
@@ -35,12 +34,8 @@
             </when>
         </conditional>
     </xml>
-    <xml name="input_files">
-        <param name="input_first_sequence" type="data" format="fastq,fastq.gz" label="First input sequence" help="The first sequence:"/>
-        <param name="input_second_sequence" type="data" format="fastq,fastq.gz" label="Second input sequence" help="The second sequence:"/>
-    </xml>
     <xml name="re1">
-        <param argument="--re1" type="text" value="" label="Restriction enzyme recognition sequence" help="Restriction enzyme recognition sequence"/>
+        <param argument="--re1" type="text" value="" label="Restriction enzyme recognition sequence" help="Restriction enzyme used e.g. A^GATCT,BglII. Some Hi-C protocols may use several enzymes. To specify several enzymes, use the ':' to separate them e.g. A^GATCT,BglII:A^AGCTT,HindIII:^GATC,DpnII. HiCUP accomodates N in restriction enzyme: e.g. :A^ANCTT"/>
     </xml>
     <xml name="re2">
         <param argument="--re2" type="text" value="" label="Restriction enzyme instead of sonication to shorten di-tags."
@@ -54,4 +49,51 @@
         <param argument="--nofill" type="boolean" value="false" truevalue="--nofill" falsevalue="" label="No fill"
             help="Hi-C protocol did NOT include a fill-in of sticky ends prior to re-ligation and therefore reads shall be truncated at the restriction site sequence"/>
     </xml>
+    <token name="@PAIRED-END_INPUT@"><![CDATA[
+    ## Taken from cutadapt except that I don't accept space in name
+    #import re
+    #set library_type = str($library.type)
+    #if $library_type == 'paired':
+        #set input_1 = $library.input_1
+        #set input_2 = $library.input_2
+    #else if $library_type == 'paired_collection'
+        #set input_1 = $library.input_1.forward
+        #set input_2 = $library.input_1.reverse
+    #end if
+    
+    #if $input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
+        #set ext = ".fq.gz"
+    #else:
+        #set ext = ".fq"
+    #end if
+    #set read1 = "dataset1" + $ext
+    ln -f -s '${input_1}' '$read1' &&
+
+    #if $input_2.is_of_type("fastq.gz", "fastqsanger.gz"):
+        #set ext2 = ".fq.gz"
+    #else:
+        #set ext2 = ".fq"
+    #end if
+    #set read2 = "dataset2" + $ext2
+    ln -f -s '${input_2}' '$read2' &&
+    ]]>
+    </token>
+    <xml name="input_paired">
+        <conditional name="library">
+            <param name="type" type="select" label="How Paired-end reads are organized">
+                <option value="paired">Separately</option>
+                <option value="paired_collection">Paired-end Collection</option>
+            </param>
+
+            <when value="paired">
+                <param name="input_1" format="fastq,fastq.gz" type="data" label="FASTQ/A file #1" help="Should be of datatype &quot;fastq.gz&quot;or &quot;fasta&quot;" />
+                <param name="input_2" format="fastq,fastq.gz" type="data" label="FASTQ/A file #2" help="Should be of datatype &quot;fastq.gz&quot;or &quot;fasta&quot;" />
+            </when>
+
+            <when value="paired_collection">
+                <param name="input_1" format="fastq,fastq.gz" type="data_collection" collection_type="paired" label="Paired Collection" help="Should be of datatype &quot;fastq.gz&quot; or &quot;fastq&quot;" />
+            </when>
+
+        </conditional>
+    </xml>
 </macros>