diff hisat2_macros.xml @ 14:526b91fbde60 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2

--- a/hisat2_macros.xml	Tue Jul 18 14:25:13 2017 -0400
+++ b/hisat2_macros.xml	Wed Jul 19 04:57:27 2017 -0400
@@ -1,52 +1,55 @@
 <?xml version="1.0"?>
 <macros>
     <xml name="single_paired_selector">
-        <param label="Single end or paired reads?" name="paired_selector" type="select">
-            <option value="paired_collection">Collection of paired reads</option>
-            <option value="paired">Individual paired reads</option>
-            <option value="single">Individual unpaired reads</option>
+        <param name="paired_selector" type="select" label="Single end or paired reads?">
+            <option value="paired">Paired reads</option>
+            <option value="single">Unpaired reads</option>
         </param>
     </xml>
     <xml name="paired_input_conditional" tokens="ftype">
         <conditional name="paired">
             <expand macro="single_paired_selector" />
-            <when value="paired_collection">
-                <param collection_type="paired" format="@FTYPE@" label="Paired reads" name="reads" type="data_collection" />
-                <expand macro="paired_end_conditional" />
-                <expand macro="paired_end_output" />
-            </when>
             <when value="paired">
-                <param format="@FTYPE@" label="Forward reads" name="reads_f" type="data" />
-                <param format="@FTYPE@" label="Reverse reads" name="reads_r" type="data" />
+                <conditional name="collection" label="Data structure">
+                    <param name="collection_selector" type="select" label="Input is structured as" help="If a list of pairs is selected, HISAT2 will run in batch mode over each pair in the list, producing a list of output bam files">
+                        <option value="files">Individual files</option>
+                        <option value="collection">Pair collection or list of pairs</option>
+                    </param>
+                    <when value="collection">
+                        <param name="reads" type="data_collection" collection_type="paired" format="@FTYPE@" label="Paired reads" />
+                    </when>
+                    <when value="files">
+                        <param name="forward" type="data" format="@FTYPE@" label="Forward reads" />
+                        <param name="reverse" type="data" format="@FTYPE@" label="Reverse reads" />
+                    </when>
+                </conditional>
                 <expand macro="paired_end_conditional" />
                 <expand macro="paired_end_output" />
             </when>
             <when value="single">
-                <param format="@FTYPE@" label="Reads" name="reads" type="data" />
-                <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" argument="--un / --un-gz" />
-                <param name="aligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" argument="--al / --al-gz" />
+                <param name="reads" type="data" format="@FTYPE@" label="Reads" />
+                <param name="unaligned_file" argument="--un-gz" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" />
+                <param name="aligned_file" argument="--al-gz" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" />
             </when>
         </conditional>
     </xml>
     <xml name="paired_end_conditional">
         <conditional name="paired_end_options">
-            <param label="Paired-end options" name="paired_end_options_selector" type="select">
+            <param name="paired_end_options_selector" type="select" label="Paired-end options">
                 <option value="defaults">Use default values</option>
                 <option value="advanced">Specify paired-end parameters</option>
             </param>
             <when value="defaults" />
             <when value="advanced">
-                <param name="no_mixed" label="Disable alignments of individual mates" type="boolean" truevalue="--no-mixed" falsevalue=""
-                    help="By default, when hisat cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates. This option disables that behavior. (--no-mixed)" />
-                <param name="no_discordant" label="Disable discordant alignments" type="boolean" truevalue="--no-discordant" falsevalue=""
-                    help="By default, hisat looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (--fr/--rf/--ff, -I, -X). This option disables that behavior. (--no-discordant)" />
-                <param name="skip_reverse" label="Skip reference strand of reference" type="boolean" truevalue="--norc" falsevalue="" help="(--norc) If --norc is specified, hisat will not attempt to align unpaired reads against the reverse-complement (Crick) reference strand. In paired-end mode, --nofw and --norc pertain to the fragments; i.e. specifying --nofw causes hisat to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand." />
+                <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" label="Disable alignments of individual mates" help="By default, when hisat cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates. This option disables that behavior" />
+                <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" label="Disable alignments of individual mates" help="By default, hisat looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (--fr/--rf/--ff, -I, -X). This option disables that behavior" />
+                <param name="skip_reverse" type="boolean" truevalue="--norc" falsevalue="" label="Skip reference strand of reference" help="If --norc is specified, hisat will not attempt to align unpaired reads against the reverse-complement (Crick) reference strand. In paired-end mode, --nofw and --norc pertain to the fragments; i.e. specifying --nofw causes hisat to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand" />
             </when>
         </conditional>
     </xml>
     <xml name="paired_end_output">
-        <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" argument="--un-conc / --un-conc-gz" />
-        <param name="aligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" argument="--al-conc / --al-conc-gz" />
+        <param name="unaligned_file" argument="--un-conc-gz" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" />
+        <param name="aligned_file" argument="--al-conc-gz" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" />
     </xml>
     <token name="@paired_end_options@">
         #if str( $input_format.paired.unaligned_file ) == "true":
@@ -66,7 +69,7 @@
             #else:
                 --al-conc '${output_aligned_reads_l}'
             #end if
-        #end if  
+        #end if
         #if str($input_format.paired.paired_end_options.paired_end_options_selector) == 'advanced':
             ${input_format.paired.paired_end_options.no_mixed}
             ${input_format.paired.paired_end_options.no_discordant}
@@ -83,49 +86,51 @@
 <![CDATA[
         #set compressed="False"
         #if str($input_format.paired.paired_selector) == 'paired':
-            #if $input_format.paired.reads_f.is_of_type("fastq.gz", "fastqsanger.gz"):
-                #set read1 = "input_f.fastq.gz"
-                #set compressed = "GZ"
-            #else if $input_format.paired.reads_f.is_of_type("fastq.bz2", "fastqsanger.bz2"):
-                #set read1 = "input_f.fastq.bz2"
-                #set compressed = "BZ2"
+            #if str($input_format.paired.collection.collection_selector) == 'collection':
+                #if $input_format.paired.collection.reads.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
+                    #set read1 = "input_f.fastq.gz"
+                    #set compressed = "GZ"
+                #else if $input_format.paired.collection.reads.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
+                    #set read1 = "input_f.fastq.bz2"
+                    #set compressed = "BZ2"
+                #else:
+                    #set read1 = "input_f.fastq"
+                #end if
+                ln -f -s '${input_format.paired.collection.reads.forward}' ${read1} &&
+
+                #if $input_format.paired.collection.reads.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
+                    #set read2 = "input_r.fastq.gz"
+                    #set compressed = "GZ"
+                #else if $input_format.paired.collection.reads.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
+                    #set read2 = "input_r.fastq.bz2"
+                    #set compressed = "BZ2"
+                #else:
+                    #set read2 = "input_r.fastq"
+                #end if
+                ln -f -s '${input_format.paired.collection.reads.reverse}' ${read2} &&
             #else:
-                #set read1 = "input_f.fastq"
-            #end if
-            ln -f -s '${input_format.paired.reads_f}' ${read1} &&
+                #if $input_format.paired.collection.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
+                    #set read1 = "input_f.fastq.gz"
+                    #set compressed = "GZ"
+                #else if $input_format.paired.collection.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
+                    #set read1 = "input_f.fastq.bz2"
+                    #set compressed = "BZ2"
+                #else:
+                    #set read1 = "input_f.fastq"
+                #end if
+                ln -f -s '${input_format.paired.collection.forward}' ${read1} &&
 
-            #if $input_format.paired.reads_r.is_of_type("fastq.gz", "fastqsanger.gz"):
-                #set read2 = "input_r.fastq.gz"
-                #set compressed = "GZ"
-            #else if $input_format.paired.reads_r.is_of_type("fastq.bz2", "fastqsanger.bz2"):
-                #set read2 = "input_r.fastq.bz2"
-                #set compressed = "BZ2"
-            #else:
-                #set read2 = "input_r.fastq"
+                #if $input_format.paired.collection.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
+                    #set read2 = "input_r.fastq.gz"
+                    #set compressed = "GZ"
+                #else if $input_format.paired.collection.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
+                    #set read2 = "input_r.fastq.bz2"
+                    #set compressed = "BZ2"
+                #else:
+                    #set read2 = "input_r.fastq"
+                #end if
+                ln -f -s '${input_format.paired.collection.reverse}' ${read2} &&
             #end if
-            ln -f -s '${input_format.paired.reads_r}' ${read2} &&
-        #else if str($input_format.paired.paired_selector) == 'paired_collection':
-            #if $input_format.paired.reads.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
-                #set read1 = "input_f.fastq.gz"
-                #set compressed = "GZ"
-            #else if $input_format.paired.reads.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
-                #set read1 = "input_f.fastq.bz2"
-                #set compressed = "BZ2"
-            #else:
-                #set read1 = "input_f.fastq"
-            #end if
-            ln -s '${input_format.paired.reads.forward}' ${read1} &&
-
-            #if $input_format.paired.reads.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
-                #set read2 = "input_r.fastq.gz"
-                #set compressed = "GZ"
-            #else if $input_format.paired.reads.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
-                #set read2 = "input_r.fastq.bz2"
-                #set compressed = "BZ2"
-            #else:
-                #set read2 = "input_r.fastq"
-            #end if
-            ln -s '${input_format.paired.reads.reverse}' ${read2} &&
         #else:
             #if $input_format.paired.reads.is_of_type("fastq.gz", "fastqsanger.gz"):
                 #set read1 = "input_f.fastq.gz"