--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Nov 25 12:37:01 2015 -0500
@@ -0,0 +1,336 @@
+<macros>
+
+    <token name="@single_or_paired_cmd@">
+        #if str( $library.type ) == "single":
+            F1=${library.input_1}
+        #elif str( $library.type ) == "paired":
+            F1=${library.input_1}
+            F2=${library.input_2}
+            SAME_HEADERS=${library.SAME_HEADERS}
+        #else
+            ## prepare paired-end collection
+            F1=${library.input_1.forward}
+            F2=${library.input_1.reverse}
+            SAME_HEADERS=${library.SAME_HEADERS}
+        #end if
+    </token>
+
+    <xml name="paired_options">
+        <when value="paired">
+            <param name="input_1" format="fastq" type="data" label="FASTQ file #1"/>
+            <param name="input_2" format="fastq" type="data" label="FASTQ file #2"/>
+            <yield />
+            <param name="SAME_HEADERS" type="boolean"
+                label="Ensure headers of both reads of a pair are identical (SAME_HEADERS)"
+                help="Only applies if barcodes are added to the header (option ADD)"
+                truevalue="true"
+                falsevalue="false" checked="false"/>
+        </when>
+        <when value="paired_collection">
+            <param name="input_1" format="fastq" type="data_collection" collection_type="paired"
+                label="FASTQ Paired Dataset"/>
+            <yield />
+            <param name="SAME_HEADERS" type="boolean"
+                label="Ensure headers of both reads of a pair are identical (SAME_HEADERS)"
+                help="Only applies if barcodes are added to the header (option ADD)"
+                truevalue="true"
+                falsevalue="false" checked="false"/>
+        </when>
+    </xml>
+
+    <token name="@single_or_paired_illu_cmd@">
+        @single_or_paired_cmd@
+        I1=$library.I1
+        #if str( $library.type ) != "single":
+            #if str( $library.I2_CONDITIONAL.I2_AVAILABLE ) == "true":
+                I2=${library.I2_CONDITIONAL.I2}
+                BRED=${library.I2_CONDITIONAL.BRED_CONDITIONAL.BRED}
+                #if str( $library.I2_CONDITIONAL.BRED_CONDITIONAL.BRED ) == "true":
+                    STRICT=${library.I2_CONDITIONAL.BRED_CONDITIONAL.STRICT}
+                #end if
+            #end if
+        #end if
+    </token>
+
+    <xml name="single_or_paired_illu">
+        <conditional name="library">
+            <param name="type" type="select" label="Is this single or paired library">
+              <option value="single">Single-end</option>
+              <option value="paired">Paired-end</option>
+              <option value="paired_collection">Paired-end Dataset Collection</option>
+            </param>
+            <when value="single">
+                <param name="input_1" format="fastq" type="data" label="FASTQ file"/>
+                <param name="I1" type="data" format="fastq" label="First Index File"/>
+            </when>
+            <expand macro="paired_options">
+                <param name="I1" type="data" format="fastq" label="First Index File"/>
+                <conditional name="I2_CONDITIONAL">
+                    <param name="I2_AVAILABLE" type="select" label="Do you have a second index file?">
+                        <option value="true">Yes</option>
+                        <option value="false" selected="true">No</option>
+                    </param>
+                    <when value="true">
+                        <param name="I2" type="data" format="fastq" label="Second Index File"/>
+                        <expand macro="bred_conditional"/>
+                    </when>
+                    <when value="false"/>
+                </conditional>
+            </expand>
+        </conditional>
+    </xml>
+
+    <xml name="single_or_paired_general">
+        <conditional name="library">
+            <param name="type" type="select" label="Is this single or paired library">
+              <option value="single">Single-end</option>
+              <option value="paired">Paired-end</option>
+              <option value="paired_collection">Paired-end Dataset Collection</option>
+            </param>
+            <when value="single">
+                <param name="input_1" format="fastq" type="data" label="FASTQ file"/>
+            </when>
+            <expand macro="paired_options">
+                <yield />
+            </expand>
+        </conditional>
+    </xml>
+
+    <token name="@demultiplex_paired_end_cmd_options@">
+        BPOS=$library.BPOS_CONDITIONAL.BPOS
+        #if str( $library.BPOS_CONDITIONAL.BPOS ) == "BOTH":
+            BM=${library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BM}
+            #if str( $library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BM ) == "BOTH":
+                BRED=${library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BRED_CONDITIONAL.BRED}
+                #if str( $library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BRED_CONDITIONAL.BRED ) == "true":
+                    STRICT=${library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BRED_CONDITIONAL.STRICT}
+                #end if
+            #end if
+        #end if
+    </token>
+
+    <xml name="demultiplex_paired_end_options">
+        <conditional name="BPOS_CONDITIONAL">
+            <param name="BPOS" type="select" label="Barcode read position (BPOS)" help="where are the barcodes">
+                <option value="READ_1" selected="true">READ_1 (beginning of read from the first fastq file)</option>
+                <option value="READ_2">READ_2 (beginning of read from the second fastq file)</option>
+                <option value="BOTH">BOTH (beginning of both reads)</option>
+            </param>
+            <when value="READ_1"/>
+            <when value="READ_2"/>
+            <when value="BOTH">
+                <conditional name="BM_CONDITIIONAL">
+                    <param name="BM" type="select" label="Barcode for sample matching (BM)"
+                        help="which barcode should be used for sample look up (BM option)." >
+                        <option value="READ_1" selected="true">
+                            READ_1 (beginning of read from the first fastq file)
+                        </option>
+                        <option value="READ_2">
+                            READ_2 (beginning of read from the second fastq file)
+                        </option>
+                        <option value="BOTH">
+                            BOTH (beginning of both reads)
+                        </option>
+                    </param>
+                    <when value="READ_1"/>
+                    <when value="READ_2"/>
+                    <when value="BOTH">
+                        <expand macro="bred_conditional"/>
+                    </when>
+                </conditional>
+            </when>
+        </conditional>
+    </xml>
+
+    <xml name="bred_conditional">
+        <conditional name="BRED_CONDITIONAL">
+            <param name="BRED" type="select" label="Redundant barcodes (BRED)"
+                help="are the barcodes REDUNDANT i.e. do they both resolve to the same sample.">
+                <option value="true" selected="true">Yes</option>
+                <option value="false">No</option>
+            </param>
+            <when value="true">
+                <param name="STRICT" type="boolean" label="Strict (S)"
+                    truevalue="true"
+                    falsevalue="false"
+                    checked="false"
+                />
+            </when>
+            <when value="false"/>
+        </conditional>
+    </xml>
+
+    <token name="@barcode_option_cmd@">
+        #if str( $barcodes.barcode_list_type_con ) == "text":
+            BARCODE_FILE=${barcode_file_from_text}
+        #else if str( $barcodes.barcode_list_type_con ) == "file":
+            BARCODE_FILE=${barcodes.BARCODE_FILE}
+        #end if
+    </token>
+
+    <xml name="barcode_option">
+        <conditional name="barcodes">
+            <param name="barcode_list_type_con" type="select" label="Barcode list input type">
+              <option value="file" selected="true">Use a tab-delimited file from the history</option>
+              <option value="text">Paste the barcodes list in a text field within the form</option>
+            </param>
+
+            <when value="file">
+                <param name="BARCODE_FILE" type="data" format="tabular,txt" label="Barcode List"
+                    help="Barcode list format: one sample per line. First column is sample name and second is the
+                    barcode, separated by tab or space. A third and fourth column can be used to specify the resulting
+                    file names. See help below."/>
+            </when>
+
+            <when value="text">
+                <param name="barcode_text" type="text" area="True" size="10x30"
+                    value="sample_name\tbarcode\n" label="Barcode List"
+                    help="Barcode list format: one sample per line. First column is sample name and second is the
+                    barcode, separated by tab or space. A third and fourth column can be used to specify the resulting
+                    file names. See help below.">
+                    <sanitizer>
+                        <valid initial="string.printable"></valid>
+                        <mapping initial="none"/>
+                    </sanitizer>
+                </param>
+            </when>
+        </conditional>
+    </xml>
+
+    <xml name="barcode_config_file">
+        <configfile name="barcode_file_from_text">#set from_text_area = ''
+#if str( $barcodes.barcode_list_type_con ) == "text":
+#set from_text_area = $barcodes.barcode_text
+#end if
+${from_text_area}</configfile>
+    </xml>
+
+    <token name="@barcode_len_cmd@">
+        #if str( $LEN ) != "":
+            BCLEN=$LEN
+        #end if
+    </token>
+
+    <xml name="barcode_len_option">
+        <param name="LEN" type="text" value="" label="Barcode Length (LEN)"
+            help="If 'Barcode read position'=BOTH and 'Redundant barcodes'=False, two distinct
+                  lengths can be provided using the syntax LEN=X:Z where X and Z are 2 integers representing
+                  the barcode length for read_1 and read_2 respectively. Default: empty"/>
+    </xml>
+    <xml name="clip_barcode">
+        <param name="CLIP_BARCODE" type="boolean" label="Remove barcode sequence from read (C)"
+           truevalue="true" falsevalue="false" checked="true"/>
+    </xml>
+
+    <token name="@demultiplexer_common_options_cmd@">
+        ADD=${ADD}
+        MM=$MM
+        MMD=$MMD
+        Q=$MIN_BASE_QUALITY
+        QUALITY_FORMAT=$QUALITY_FORMAT
+    </token>
+    <xml name="demultiplexer_common_options">
+        <param name="ADD" type="boolean"
+            label="Add matched barcode at the end of the read header (ADD)"
+            truevalue="true"
+            falsevalue="false"
+            checked="true"
+        />
+        <param name="MM" type="text" value="1" label="Maximum Mismatches (MM)"
+            help="Maximum mismatches for a barcode to be considered a match." />
+
+        <param name="MMD" type="text" value="1" label="Minimum mismatch difference (MMD)"
+            help="Minimum difference between number of mismatches in the best and second best barcodes for a barcode
+            to be considered a match." />
+
+        <param name="MIN_BASE_QUALITY" type="text" value="10" label="Minimum base quality (Q)"
+            help="Any barcode bases falling below this quality will be
+            considered a mismatch even in the bases match." />
+
+        <param name="QUALITY_FORMAT" type="select" label="Fastq Quality Format (V)"
+            help="How are the quality values encoded in the fastq.  Either 'Solexa' for
+            pre-pipeline 1.3 style scores (solexa scaling + 66), 'Illumina' for pipeline 1.3 and
+            above (phred scaling + 64) or 'Standard' for phred scaled scores with a character shift
+            of 33.">
+            <option value="Standard" selected="true">
+                Fastq - Illumina Casava v1.8 with Sanger coding quality (phred scaling + 33)
+            </option>
+            <option value="Illumina">
+                Fastq - Illumina v1.3 or above coding of quality (phred scaling + 64)
+            </option>
+            <option value="Solexa">
+                Fastq - Solexa-style quality (solexa scaling + 66)
+            </option>
+            <option value="null">
+                Detect automatically
+            </option>
+        </param>
+    </xml>
+
+    <token name="@demultiplexer_common_output_options_cmd@">
+        KEEP_UNASSIGNED_READ=$KEEP_UNASSIGNED_READ
+        STATS_ONLY=${adv_options.STATS_ONLY}
+        #if str( $adv_options.DIAG ) == "true":
+            BARCODE_DIAG_FILE=$BARCODE_DIAG_FILE
+        #end if
+    </token>
+    <xml name="demultiplexer_common_output_options">
+        <param name="KEEP_UNASSIGNED_READ" type="boolean" label="Keep unassigned reads (KEEP_UNASSIGNED_READ)"
+            truealue="true"
+            falsevalue="false"
+            checked="true"
+        />
+        <section name="adv_options" title="Advanced Options" expanded="False">
+            <param name="DIAG" type="boolean" label="Output barcode match reporting file (DIAG)"
+                truevalue="true" falsevalue="false" checked="false"
+                help="This file will
+                      contain a line per read pair with the barcode best matching the read subsequence or 'null' when no
+                      match is found according to matching parameters. This file is useful for debugging or further
+                      processing in case both ends are barcoded."/>
+            <param name="STATS_ONLY" type="boolean" label="Only produce metric and diagnostic reports (STATS_ONLY)"
+                truevalue="true" falsevalue="false" checked="false"
+                help="do not demultiplex." />
+        </section>
+    </xml>
+
+    <token name="@common_options_cmd@">
+        XT=${XT}
+        ZT=${ZT}
+        #if str( $RCHAR ) != "":
+            RCHAR=${RCHAR}
+        #end if
+        GZ=${GZ}
+        OUTPUT_DIR=results
+    </token>
+    <xml name="common_options">
+        <param name="XT" type="text" value="0"
+            label="Extra number of bases to be trimmed right after the barcode (XT)" />
+        <param name="ZT" type="text" value="0"
+            label="Extra number of bases to be trimmed from the read end (ZT)" />
+
+        <param name="RCHAR" type="text"
+            label="Replace white space in the read name/header with speficied symbols (RCHAR)"
+            help="Set to empty for no replacement"
+            value=":"/>
+
+        <param name="GZ" type="boolean" hidden="true" label="Compress output (GZ)"
+            help="will result in fastq.gz files."
+            truevalue="true"
+            falsevalue="false"
+            checked="false"/>
+    </xml>
+
+    <token name="@demultiplexer_common_outputs_cmd@">
+        METRICS_FILE_NAME=$METRICS_FILE_NAME
+    </token>
+    <xml name="demultiplexer_common_outputs">
+        <data name="METRICS_FILE_NAME" format="tabular" label="Je-Demultiplex result">
+            <!--<discover_datasets pattern="(?P&lt;name&gt;.*)\.txt" ext="fastqsanger"-->
+            <discover_datasets pattern="(?P&lt;name&gt;.*)\.txt" directory="results" visible="true" ext="fastqsanger"/>
+        </data>
+        <data name="BARCODE_DIAG_FILE" format="tabular" label="Barcode statistics">
+            <filter>(adv_options['DIAG'] == 'true')</filter>
+        </data>
+    </xml>
+
+</macros>