# HG changeset patch
# User jjohnson
# Date 1629385868 0
# Node ID 6137ff37bea11b33bc9521ef72d988f12b8460f9
# Parent  4635a93ebd9100ee56014a5740348ed48d284e45
"planemo upload commit 77a5370a0978b5332bb3a9f063588a52a468ea08"

diff -r 4635a93ebd91 -r 6137ff37bea1 fgbio_fastq_to_bam.xml
--- a/fgbio_fastq_to_bam.xml	Wed Feb 24 13:01:53 2021 +0000
+++ b/fgbio_fastq_to_bam.xml	Thu Aug 19 15:11:08 2021 +0000
@@ -6,16 +6,11 @@
     <expand macro="requirements" />
     <version_command>fgbio --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
+        @LINK_FASTQ_INPUTS@
         fgbio FastqToBam 
-        --input 
-        #for $input in $inputs
-            '$input'
-        #end for
+        @FASTQ_INPUTS@
         --sample='$sample'
         --library='$library'
-        #if $read_structures:
-            --read-structures $read_structures
-        #end if
         --sort='$sort'
         --output '$output'
         ## optional bam header content
@@ -51,13 +46,12 @@
         #end if
     ]]></command>
     <inputs>
-        <param name="inputs" type="data" format="fastq" multiple="true" label="Fastq files corresponding to each sequencing read"/>
+        <expand macro="fastq_inputs"/>
         <param argument="--sample" type="text" value="" label="The name of the sequenced sample">
+            <validator type="empty_field"/>
         </param>
         <param argument="--library" type="text" value="" label="The name/ID of the sequenced library">
-        </param>
-        <param argument="--read-structures" type="text" value="" optional="true" label="Read structures, one for each of the FASTQ">
-            <expand macro="read_structures_validator" />
+            <validator type="empty_field"/>
         </param>
         <param argument="--sort" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Sort bam by queryname" 
                help="If true, queryname sort the BAM file, otherwise preserve input order."/>
diff -r 4635a93ebd91 -r 6137ff37bea1 macros.xml
--- a/macros.xml	Wed Feb 24 13:01:53 2021 +0000
+++ b/macros.xml	Thu Aug 19 15:11:08 2021 +0000
@@ -1,18 +1,205 @@
 <macros>
     <token name="@TOOL_VERSION@">1.3.0</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">fgbio</requirement>
             <yield/>
         </requirements>
     </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">@online{fgbio,
+              author = {Tim Fennell, Nils Homer},
+              title = {fgbio},
+              year = 2015,
+              url = {https://github.com/fulcrumgenomics/fgbio},
+              urldate = {2021-03-01}
+            }</citation>
+        </citations>
+    </xml>
     <token name="@READ_STRUCTURE_PATTERN@">(([1-9][0-9]*[TBMS])*([+]|[1-9][0-9]*)[TBMS])</token>
     <token name="@READ_STRUCTURES_PATTERN@">@READ_STRUCTURE_PATTERN@(\s@READ_STRUCTURE_PATTERN@)*</token>
-    <xml name="read_structures_validator">
+    <xml name="read_structures_validator" token_pattern="@READ_STRUCTURES_PATTERN@">
             <validator type="regex" message="">^@READ_STRUCTURES_PATTERN@$</validator>
     </xml>
+    <xml name="read_structures" token_pattern="@READ_STRUCTURES_PATTERN@">
+        <param argument="--read-structures" type="text" value="" optional="true" label="Read structures, one for each of the FASTQ">
+            <expand macro="read_structures_validator" pattern="@READ_STRUCTURE_PATTERN@" />
+        </param>
+    </xml>
+
+    <xml name="fastq_input" token_fastqtype="reads" token_defaultpaired="True" token_defaultnone="False">
+        <conditional name="@FASTQTYPE@">
+            <param name="type" type="select" label="Library type of FASTQ @FASTQTYPE@">
+                <option value="none" selected="@DEFAULTNONE@">NO fastq @FASTQTYPE@</option>
+                <option value="single">Single-end</option>
+                <option value="paired" selected="@DEFAULTPAIRED@">Paired-end</option>
+                <option value="paired_collection">Paired-end Dataset Collection</option>
+            </param>
+            <when value="none"/>
+            <when value="single">
+                <param name="input_single" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
+                <expand macro="read_structures" pattern="@READ_STRUCTURE_PATTERN@" />
+            </when>
+            <when value="paired">
+                <param name="input_read1" type="data" format="fastq,fastq.gz" label="Reads #1 in FASTQ format" />
+                <param name="input_read2" type="data" format="fastq,fastq.gz" label="Reads #2 in FASTQ format" />
+                <expand macro="read_structures" pattern="@READ_STRUCTURES_PATTERN@" />
+            </when>
+            <when value="paired_collection">
+                <param name="input_readpair" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Paired Reads in FASTQ format" />
+                <expand macro="read_structures" pattern="@READ_STRUCTURES_PATTERN@" />
+            </when>
+        </conditional>
+    </xml>
+    <xml name="fastq_reads">
+        <expand macro="fastq_input" fastqtype="reads" defaultpaired="True" defaultnone="False"/>
+    </xml>
+    <xml name="fastq_inputs">
+        <expand macro="fastq_input" fastqtype="reads" defaultpaired="True" defaultnone="False"/>
+        <expand macro="fastq_input" fastqtype="indices" defaultpaired="False" defaultnone="True"/>
+    </xml>
+    <token name="@FASTQ_READS@"><![CDATA[
+        #set $fastqs = []
+        #set $read_structs = []
+        #if $reads.type == 'single':
+            $fastqs.append($reads.input_single)
+        #elif $reads.type == 'paired':
+            $fastqs.append($reads.input_read1)
+            $fastqs.append($reads.input_read2)
+        #elif $reads.type == 'paired_collection':
+            $fastqs.append($reads.input_readpair.forward)
+            $fastqs.append($reads.input_readpair.reverse)
+        #end if
+        #if $reads.type !='none' and $reads.read_structures:
+            $read_structs.append(str($reads.read_structures))
+        #end if
+        #set $read_structures = "%s" % (' '.join($read_structs))
+        #if $read_structs:
+            --read-structures $read_structures
+        #end if
+]]></token>
+    <token name="@LINK_FASTQ_INPUTS@"><![CDATA[
+#import re
+#def identifier_or_name($input1)
+    #if hasattr($input1, 'element_identifier')
+        #return $input1.element_identifier
+    #else
+        #return $input1.name
+    #end if
+#end def
+#def clean($name1)
+    #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](fq|fastq)$','', $re.sub('.*/','', $name1.rstrip('.gz'))))
+    #return $name_clean
+#end def
+#def ln_name($ds)
+    #set $ext = ''
+    #if $ds.is_of_type('mzml') or $ds.is_of_type('fastq.gz')
+        #set $ext = ".fastq.gz"
+    #else if $ds.is_of_type('fastq')
+        #set $ext = ".fastq"
+    #end if
+    #set $name = "%s%s" % ($clean($identifier_or_name($ds)),$ext)
+    #return $name
+#end def
+        #set $fastqs = []
+        #set $read_structs = []
+        #if $reads.type == 'single':
+            #set $i_name = $ln_name($reads.input_single)
+            #silent $fastqs.append($i_name)
+            ln -s '$reads.input_single' '$i_name' &&
+        #elif $reads.type == 'paired':
+            #set $f_name = $ln_name($reads.input_read1)
+            #silent $fastqs.append($f_name)
+            ln -s '$reads.input_read1' '$f_name' &&
+            #set $r_name = $ln_name($reads.input_read2)
+            #silent $fastqs.append($r_name)
+            ln -s '$reads.input_read2' '$r_name' &&
+        #elif $reads.type == 'paired_collection':
+            #set $f_name = $ln_name($reads.input_readpair.forward)
+            #silent $fastqs.append($f_name)
+            ln -s '$reads.input_readpair.forward' '$f_name' &&
+            #set $r_name = $ln_name($reads.input_readpair.reverse)
+            #silent $fastqs.append($r_name)
+            ln -s '$reads.input_readpair.reverse' '$r_name' &&
+        #end if
+        #if $reads.type !='none' and $reads.read_structures:
+            $read_structs.append(str($reads.read_structures))
+        #end if
+        #if $indices.type == 'single':
+            #set $i_name = $ln_name($indices.input_single)
+            #silent $fastqs.append($i_name)
+            ln -s '$indices.input_single' '$i_name' &&
+        #elif $indices.type == 'paired':
+            #set $f_name = $ln_name($indices.input_read1)
+            #silent $fastqs.append($f_name)
+            ln -s '$indices.input_read1' '$f_name' &&
+            #set $r_name = $ln_name($indices.input_read2)
+            #silent $fastqs.append($r_name)
+            ln -s '$indices.input_read2' '$r_name' &&
+        #elif $indices.type == 'paired_collection':
+            #set $f_name = $ln_name($indices.input_readpair.forward)
+            #silent $fastqs.append($f_name)
+            ln -s '$indices.input_readpair.forward' '$f_name' &&
+            #set $r_name = $ln_name($indices.input_readpair.reverse)
+            #silent $fastqs.append($r_name)
+            ln -s '$indices.input_readpair.reverse' '$r_name' &&
+        #end if
+        #if $indices.type != 'none' and $indices.read_structures:
+            $read_structs.append(str($indices.read_structures))
+        #end if
+]]></token>
+    <token name="@FASTQ_INPUTS@"><![CDATA[
+        --input 
+        #for $input in $fastqs
+            '$input'
+        #end for
+        #set $read_structures = "%s" % (' '.join($read_structs))
+        #if $read_structs:
+            --read-structures $read_structures
+        #end if
+]]></token>
+        <xml name="inherit_format_1">
+            <actions>
+                <conditional name="library.type">
+                    <when value="single">
+                        <action type="format">
+                            <option type="from_param" name="library.input_1" param_attribute="ext" />
+                        </action>
+                    </when>
+                    <when value="paired">
+                        <action type="format">
+                            <option type="from_param" name="library.input_1" param_attribute="ext" />
+                        </action>
+                    </when>
+                    <when value="paired_collection">
+                        <action type="format">
+                            <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
+                        </action>
+                    </when>
+                </conditional>
+            </actions>
+        </xml>
+
+        <xml name="inherit_format_2">
+            <actions>
+                <conditional name="library.type">
+                    <when value="paired">
+                        <action type="format">
+                            <option type="from_param" name="library.input_2" param_attribute="ext" />
+                        </action>
+                    </when>
+                    <when value="paired_collection">
+                        <action type="format">
+                            <option type="from_param" name="library.input_1" param_attribute="reverse.ext" />
+                        </action>
+                    </when>
+                </conditional>
+            </actions>
+        </xml>
     <xml name="sam_tag_validator">
+
             <validator type="regex" message="">^[A-Za-z][A-Za-z]$</validator>
     </xml>
     <xml name="sam_sort_order">
diff -r 4635a93ebd91 -r 6137ff37bea1 macros.xml.bak
--- a/macros.xml.bak	Wed Feb 24 13:01:53 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,56 +0,0 @@
-<macros>
-    <token name="@TOOL_VERSION@">1.3.0</token>
-    <token name="@VERSION_SUFFIX@">0</token>
-    <xml name="requirements">
-        <requirements>
-            <requirement type="package" version="@TOOL_VERSION@">fgbio</requirement>
-            <yield/>
-        </requirements>
-    </xml>
-    <token name="@READ_STRUCTURE_PATTERN@">(([1-9][0-9]*[TBMS])*([+]|[1-9][0-9]*)[TBMS])</token>
-    <token name="@READ_STRUCTURES_PATTERN@">@READ_STRUCTURE_PATTERN@(\s@READ_STRUCTURE_PATTERN@)*</token>
-    <xml name="read_structures_validator">
-            <validator type="regex" message="">^@READ_STRUCTURES_PATTERN@$</validator>
-    </xml>
-    <xml name="sam_tag_validator">
-            <validator type="regex" message="">^[A-Za-z][A-Za-z]$</validator>
-    </xml>
-    <xml name="sam_sort_order">
-        <param argument="--sort-order" type="select" optional="true" label="Sort BAM by">
-            <option value="Coordinate">Coordinate</option>
-            <option value="Queryname">Queryname</option>
-            <option value="Random">Random</option>
-            <option value="RandomQuery">RandomQuery</option>
-        </param>
-    </xml>
-
-    <token name="@READ_STRUCTURES_HELP@"><![CDATA[
-**Read Structures**
-
-Read structures are made up of <number><operator> pairs much like the CIGAR string in BAM files. Four kinds of operators are recognized:
-
-    - T identifies a template read
-    - B identifies a sample barcode read
-    - M identifies a unique molecular index read
-    - S identifies a set of bases that should be skipped or ignored
-
-The last <number><operator> pair may be specified using a + sign instead of number to denote “all remaining bases”. This is useful if, e.g., fastqs have been trimmed and contain reads of varying length. For example to convert a paired-end run with an index read and where the first 5 bases of R1 are a UMI and the second five bases are monotemplate you might specify:
-
-:: 
-
-    --input r1.fq r2.fq i1.fq --read-structures 5M5S+T +T +B
-
-Alternative if you know your reads are of fixed length you could specify:
-
-:: 
-
-    --input r1.fq r2.fq i1.fq --read-structures 5M5S65T 75T 8B
-
-
-]]></token>
-    <xml name="citations">
-        <citations>
-            <yield />
-        </citations>
-    </xml>
-</macros>