changing link names

tools/halfdeep/halfdeep.xml

@@ -1,11 +1,11 @@
 <tool id="halfdeep" name="HalfDeep" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
-    <description>identifies genomic regions with half-depth coverage based on sqeuencing read mappings. These regions may reveal insights into heterogametic sex chromosomes, haplotype-specific variation, or potential assembly errors such as heterotypic duplications.</description>
+    <description>identifies genomic regions with half-depth coverage based on sequencing read mappings.</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
-        #import os
+        #import re
         ##
         ## reference
         ##
@@ -18,16 +18,16 @@
         #set $mapped_reads_dir = "halfdeep/ref/mapped_reads"
         mkdir -p '$reads_dir' '$mapped_reads_dir' &&
         #for $read in $reads
-            #set $seq_base = os.path.basename(str($read))
-            ln -s '$read' '$reads_dir/$seq_base' &&
-            echo '$reads_dir/$seq_base' >> input.fofn &&
+            #set $read_base = re.sub('[^\w\-\s]', '_', str($read.element_identifier))
+            ln -s '$read' '$reads_dir/${read_base}.$read.ext' &&
+            echo '$reads_dir/${read_base}.$read.ext' >> input.fofn &&
             ##
             ## mapped reads
             ##
             #for $mapped_read in $mapped_reads
-                ln -s '$mapped_read' "$mapped_reads_dir/${seq_base}.bam" &&
-                ln -s "${seq_base}.bam" "$mapped_reads_dir/${seq_base}.sort.bam" &&
-                ln -s '$mapped_read.metadata.bam_index' "$mapped_reads_dir/${seq_base}.sort.bam.bai" &&
+                ln -s '$mapped_read' "$mapped_reads_dir/${read_base}.bam" &&
+                ln -s "${read_base}.bam" "$mapped_reads_dir/${read_base}.sort.bam" &&
+                ln -s '$mapped_read.metadata.bam_index' "$mapped_reads_dir/${read_base}.sort.bam.bai" &&
             #end for
         #end for
         ##
@@ -43,7 +43,7 @@
     ]]></command>
     <inputs>
         <param name="ref" type="data" format="fasta,fasta.gz" label="Genome Assembly" help="A Genome Assembly in FASTA format."/>
-        <param name="reads" type="data" format="fastqsanger,fastqsanger.gz" multiple="true" label="Sequencing Reads" help="Sequencing Reads for the Genome Assembly in FASTQ format."/>
+        <param name="reads" type="data" format="fastqsanger,fastqsanger.bz2,fastqsanger.gz" multiple="true" label="Sequencing Reads" help="Sequencing Reads for the Genome Assembly in FASTQ format."/>
         <param name="mapped_reads" type="data" format="bam" multiple="true" label="Aligned Reads" help="Alignments of the Sequencing Reads to the Genome Assembly in BAM format."/>
     </inputs>
     <outputs>
@@ -64,35 +64,28 @@
         </test>
     </tests>
     <help><![CDATA[
-HalfDeep requires the following inputs:
 
-1. A genome assembly in FASTA format.
+HalfDeep identifies genomic regions with half-depth coverage based on sequencing read mappings. These regions may reveal insights into heterogametic sex chromosomes, haplotype-specific variation, or potential assembly errors such as heterotypic duplications.
 
-2. Reads in FASTQ format.
+Given the following three inputs:
 
+1. A genome assembly in FASTA format.
+2. Reads in FASTQ format.
 3. Mapped reads in BAM format
 
-
 HalfDeep automates the following tasks:
 
 1. Mapping reads and merging individual mapping files.
-
 2. Calculating per-base read depth.
-
 3. Smoothing read coverage using a defined window with genodsp.
-
 4. Determining the percentile of read coverage.
-
 5. Identifying genomic regions with half-depth coverage based on a specified percentile threshold (e.g., 40–60%) and exporting them in BED file forma
 
 HalfDeep produces the following outputs:
 
 1. Scaffold lengths: A tabular file containing the name and legth of each sequence in the genome assembly.
-
 2. Depths: A tabular file containing the read depts.
-
 3. A tabular file containing the name and legth of each sequence in the genome assembly: stuff
-
 4. HalfDeep: BED file containina regions of the genome assembly that are "covered at half depth"
     ]]></help>
     <expand macro="citations"/>