--- a/picard_FastqToSam.xml	Mon Sep 25 08:32:17 2023 +0000
+++ b/picard_FastqToSam.xml	Sun Mar 03 16:06:11 2024 +0000
@@ -1,13 +1,13 @@
-<tool name="FastqToSam" id="picard_FastqToSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="20.01">
+<tool name="FastqToSam" id="picard_FastqToSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
     <description>convert Fastq data into unaligned BAM</description>
     <macros>
         <import>picard_macros.xml</import>
-        <token name="@WRAPPER_VERSION@">2</token>
+        <token name="@WRAPPER_VERSION@">0</token>
     </macros>
     <xrefs>
         <xref type="bio.tools">picard_fastqtosam</xref>
     </xrefs>
-    <expand macro="requirements" />
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
     @java_options@
     #if str( $input_type.input_type_selector ) == "se":
@@ -24,145 +24,138 @@
     #if $fwd.ext.endswith(".gz")
       gunzip -c '$fwd' > fwd.fastq &&
     #else
-      ln -s '$fwd' fwd.fastq &&
+      ln -sf '$fwd' fwd.fastq &&
     #end if
     #if rev
       #if rev.ext.endswith(".gz")
         gunzip -c '$rev' > rev.fastq &&
       #else
-        ln -s '$rev' rev.fastq &&
+        ln -sf '$rev' rev.fastq &&
       #end if
     #end if
    
-    picard
-    FastqToSam
+    picard FastqToSam
 
-    FASTQ=fwd.fastq
+    --FASTQ fwd.fastq
     #if rev
-      FASTQ2=rev.fastq
+      --FASTQ2 rev.fastq
     #end if
 
     #if $fwd.ext.startswith("fastqillumina")
-      QUALITY_FORMAT="Illumina"
+      --QUALITY_FORMAT "Illumina"
     #else if $fwd.ext.startswith("fastqsolexa")
-      QUALITY_FORMAT="Solexa"
+      --QUALITY_FORMAT "Solexa"
     #else 
-      QUALITY_FORMAT="Standard"
+      --QUALITY_FORMAT "Standard"
     #end if
-    OUTPUT="${outFile}"
-    READ_GROUP_NAME="${read_group_name}"
-    SAMPLE_NAME="${sample_name}"
+    --OUTPUT '${outFile}'
+    --READ_GROUP_NAME '${read_group_name}'
+    --SAMPLE_NAME '${sample_name}'
 
     #if str( $library_name ):
-      LIBRARY_NAME="${library_name}"
+        --LIBRARY_NAME '${library_name}'
     #end if
 
     #if str( $platform_unit ):
-      PLATFORM_UNIT="${platform_unit}"
+        --PLATFORM_UNIT '${platform_unit}'
     #end if
 
     #if str( $platform ):
-      PLATFORM="${platform}"
+        --PLATFORM '${platform}'
     #end if
 
     #if str( $sequencing_center ):
-      SEQUENCING_CENTER="${sequencing_center}"
+        --SEQUENCING_CENTER '${sequencing_center}'
     #end if
 
     #if str( $predicted_insert_size ):
-      PREDICTED_INSERT_SIZE="${predicted_insert_size}"
+        --PREDICTED_INSERT_SIZE '${predicted_insert_size}'
     #end if
 
     #if str( $comment ):
-      COMMENT="${comment}"
+        --COMMENT '${comment}'
     #end if
 
     #if str( $description ):
-      DESCRIPTION="${description}"
+        --DESCRIPTION '${description}'
     #end if
 
     #if str( $run_date ):
-      RUN_DATE="${run_date}"
+        --RUN_DATE '${run_date}'
     #end if
 
-    MIN_Q="${min_q}"
-    MAX_Q="${max_q}"
-    STRIP_UNPAIRED_MATE_NUMBER="${strip_unpairied_mate_number}"
-    ALLOW_AND_IGNORE_EMPTY_LINES="${allow_and_ignore_empty_lines}"
+    --MIN_Q '${min_q}'
+    --MAX_Q '${max_q}'
+    --STRIP_UNPAIRED_MATE_NUMBER '${strip_unpairied_mate_number}'
+    --ALLOW_AND_IGNORE_EMPTY_LINES '${allow_and_ignore_empty_lines}'
 
-    SORT_ORDER=coordinate
-    VALIDATION_STRINGENCY="${validation_stringency}"
-    QUIET=true
-    VERBOSITY=ERROR
-  ]]></command>
-  <inputs>
-    <conditional name="input_type">
-      <param name="input_type_selector" type="select" label="What is your input data" help="Select between single end, paired end, and collections. See help below for full explanation of dataset types">
-        <option value="se">Single end (single dataset)</option>
-        <option value="pe">Paired end (two datasets)</option>
-        <option value="pc">Paired collection</option>
-      </param>
-      <when value="se">
-        <param name="fastq" type="data" format="fastq,fastq.gz" label="Input fastq file for single end data" help="FASTQ"/>
-      </when>
-      <when value="pe">
-        <param name="fastq" type="data" format="fastq,fastq.gz" label="Input fastq file for the first read in paired end data" help="FASTQ"/>
-        <param name="fastq2" type="data" format="fastq,fastq.gz" label="Input fastq file for the second read of paired end data" help="FASTQ2"/>
-      </when>
-      <when value="pc">
-        <param name="fastq" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="FASTQ paired dataset collection" help="FASTQ and FASTQ2; A collection of two datasets with forward and reverse reads. See help below on explanation of dataset collections"/>
-      </when>
-    </conditional>
-
-    <param name="read_group_name" type="text" value="A" label="Read group name" help="READ_GROUP_NAME"/>
-    <param name="sample_name" type="text" value="sample-a" label="Sample name" help="SAMPLE_NAME"/>
-    <param name="library_name" type="text" optional="True" label="The library name" help="LIBRARY_NAME; Optional"/>
-    <param name="platform_unit" type="text" optional="True"  label="The platform unit (often run_barcode.lane)" help="PLATFORM_UNIT; Optional"/>
-    <param name="platform" type="text" optional="True"  label="The platform type (e.g. illumina, 454)" help="PLATFORM; Optional"/>
-    <param name="sequencing_center" type="text" optional="True"  label="The sequencing center from which the data originated" help="SEQUENCING_CENTER; Optional"/>
+    --SORT_ORDER coordinate
+    --VALIDATION_STRINGENCY '${validation_stringency}'
+    --QUIET true
+    --VERBOSITY ERROR
 
-    <param name="predicted_insert_size" type="integer" min="0" max="100000" optional="True" label="Predicted median insert size, to insert into the read group header" help="PREDICTED_INSERT_SIZE; Optional"/>
-    <param name="comment" type="text" optional="True" label="Comment to include in the output dataset's header" help="COMMENT; Optional"/>
-    <param name="description" type="text" optional="True" label="Optional description information" help="DESCRIPTION; Optional"/>
-    <param name="run_date" optional="True" type="text" label="Run date" help="RGDT; Optional; Format=YYYY-MM-DD (eg 1997-07-16)"/>
-    <param name="min_q" type="integer" value="0" min="0" max="100" label="Minimum quality allowed in the input fastq" help="MIN_Q; An exception will be thrown if a quality is less than this value; default=0"/>
-    <param name="max_q" type="integer" value="93" min="0" max="100" label="Minimum quality allowed in the input fastq" help="MAX_Q; An exception will be thrown if a quality is greater than this value; default=93"/>
-    <param name="strip_unpairied_mate_number" type="boolean" truevalue="true" falsevalue="false" label="If true and this is an unpaired fastq any occurance of '/1' will be removed from the end of a read name" help="STRIP_UNPAIRED_MATE_NUMBER; default=false"/>
-    <param name="allow_and_ignore_empty_lines" type="boolean" truevalue="true" falsevalue="false" label="Allow (and ignore) empty lines" help="ALLOW_AND_IGNORE_EMPTY_LINES; default=false"/>
-
-    <expand macro="VS" />
-
-  </inputs>
-
-  <outputs>
-    <data format="unsorted.bam" name="outFile" label="${tool.name} on ${on_string}: reads as unaligned BAM"/>
-  </outputs>
-
-  <tests>
-    <test>
-      <param name="input_type_selector" value="pe" />
-      <param name="read_group_name" value="A" />
-      <param name="sample_name" value="sample-a" />
-      <param name="library_name" value="A"/>
-      <param name="platform_unit" value="A"/>
-      <param name="platform" value="Illumina"/>
-      <param name="sequencing_center" value="A"/>
-      <param name="predicted_insert_size" value="300"/>
-      <param name="comment" value="A"/>
-      <param name="description" value="A"/>
-      <param name="run_date" value="2014-10-10"/>
-      <param name="min_q" value="0" />
-      <param name="max_q" value="93" />
-      <param name="strip_unpairied_mate_number" value="False" />
-      <param name="allow_and_ignore_empty_lines" value="False" />
-      <param name="validation_stringency" value="LENIENT"/>
-      <param name="fastq" value="picard_FastqToSam_read1.fq.gz" ftype="fastq.gz" />
-      <param name="fastq2" value="picard_FastqToSam_read2.fq.gz" ftype="fastq.gz" />
-      <output name="outFile" file="picard_FastqToSam_test1.bam" ftype="unsorted.bam" lines_diff="4"/>
-    </test>
-  </tests>
-
-  <help>
+  ]]></command>
+    <inputs>
+        <conditional name="input_type">
+            <param name="input_type_selector" type="select" label="What is your input data" help="Select between single end, paired end, and collections. See help below for full explanation of dataset types">
+                <option value="se">Single end (single dataset)</option>
+                <option value="pe">Paired end (two datasets)</option>
+                <option value="pc">Paired collection</option>
+            </param>
+            <when value="se">
+                <param name="fastq" type="data" format="fastq,fastq.gz" label="Input fastq file for single end data" help="FASTQ"/>
+            </when>
+            <when value="pe">
+                <param name="fastq" type="data" format="fastq,fastq.gz" label="Input fastq file for the first read in paired end data" help="FASTQ"/>
+                <param name="fastq2" type="data" format="fastq,fastq.gz" label="Input fastq file for the second read of paired end data" help="FASTQ2"/>
+            </when>
+            <when value="pc">
+                <param name="fastq" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="FASTQ paired dataset collection" help="FASTQ and FASTQ2; A collection of two datasets with forward and reverse reads. See help below on explanation of dataset collections"/>
+            </when>
+        </conditional>
+        <param name="read_group_name" type="text" value="A" label="Read group name" help="READ_GROUP_NAME"/>
+        <param name="sample_name" type="text" value="sample-a" label="Sample name" help="SAMPLE_NAME"/>
+        <param name="library_name" type="text" optional="True" label="The library name" help="LIBRARY_NAME; Optional"/>
+        <param name="platform_unit" type="text" optional="True" label="The platform unit (often run_barcode.lane)" help="PLATFORM_UNIT; Optional"/>
+        <param name="platform" type="text" optional="True" label="The platform type (e.g. illumina, 454)" help="PLATFORM; Optional"/>
+        <param name="sequencing_center" type="text" optional="True" label="The sequencing center from which the data originated" help="SEQUENCING_CENTER; Optional"/>
+        <param name="predicted_insert_size" type="integer" min="0" max="100000" optional="True" label="Predicted median insert size, to insert into the read group header" help="PREDICTED_INSERT_SIZE; Optional"/>
+        <param name="comment" type="text" optional="True" label="Comment to include in the output dataset's header" help="COMMENT; Optional"/>
+        <param name="description" type="text" optional="True" label="Optional description information" help="DESCRIPTION; Optional"/>
+        <param name="run_date" optional="True" type="text" label="Run date" help="RGDT; Optional; Format=YYYY-MM-DD (eg 1997-07-16)"/>
+        <param name="min_q" type="integer" value="0" min="0" max="100" label="Minimum quality allowed in the input fastq" help="MIN_Q; An exception will be thrown if a quality is less than this value; default=0"/>
+        <param name="max_q" type="integer" value="93" min="0" max="100" label="Minimum quality allowed in the input fastq" help="MAX_Q; An exception will be thrown if a quality is greater than this value; default=93"/>
+        <param name="strip_unpairied_mate_number" type="boolean" truevalue="true" falsevalue="false" label="If true and this is an unpaired fastq any occurance of '/1' will be removed from the end of a read name" help="STRIP_UNPAIRED_MATE_NUMBER; default=false"/>
+        <param name="allow_and_ignore_empty_lines" type="boolean" truevalue="true" falsevalue="false" label="Allow (and ignore) empty lines" help="ALLOW_AND_IGNORE_EMPTY_LINES; default=false"/>
+        <expand macro="VS"/>
+    </inputs>
+    <outputs>
+        <data format="unsorted.bam" name="outFile" label="${tool.name} on ${on_string}: reads as unaligned BAM"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_type_selector" value="pe"/>
+            <param name="read_group_name" value="A"/>
+            <param name="sample_name" value="sample-a"/>
+            <param name="library_name" value="A"/>
+            <param name="platform_unit" value="A"/>
+            <param name="platform" value="Illumina"/>
+            <param name="sequencing_center" value="A"/>
+            <param name="predicted_insert_size" value="300"/>
+            <param name="comment" value="A"/>
+            <param name="description" value="A"/>
+            <param name="run_date" value="2014-10-10"/>
+            <param name="min_q" value="0"/>
+            <param name="max_q" value="93"/>
+            <param name="strip_unpairied_mate_number" value="False"/>
+            <param name="allow_and_ignore_empty_lines" value="False"/>
+            <param name="validation_stringency" value="LENIENT"/>
+            <param name="fastq" value="picard_FastqToSam_read1.fq.gz" ftype="fastq.gz"/>
+            <param name="fastq2" value="picard_FastqToSam_read2.fq.gz" ftype="fastq.gz"/>
+            <output name="outFile" file="picard_FastqToSam_test1.bam" ftype="unsorted.bam" lines_diff="4"/>
+        </test>
+    </tests>
+    <help>
 
 .. class:: infomark
 
@@ -237,5 +230,5 @@
 @more_info@
 
   </help>
-  <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>