--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FPKM_count.xml	Tue Mar 14 10:23:21 2017 -0400
@@ -0,0 +1,132 @@
+<tool id="rseqc_FPKM_count" name="FPKM Count" version="@WRAPPER_VERSION@">
+    <description>calculates raw read count, FPM, and FPKM for each gene</description>
+
+    <macros>
+        <import>rseqc_macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+
+    <expand macro="stdio" />
+
+    <version_command><![CDATA[FPKM_count.py --version]]></version_command>
+
+    <command><![CDATA[
+        ln -sf '${input}' 'local_input.bam' &&
+        ln -sf '${input.metadata.bam_index}' 'local_input.bam.bai' &&
+        FPKM_count.py -i 'local_input.bam' -o output -r '${refgene}'
+
+        #if str($strand_type.strand_specific) == "pair"
+            -d
+            #if str($strand_type.pair_type) == "sd"
+                '1++,1--,2+-,2-+'
+            #else
+                '1+-,1-+,2++,2--'
+            #end if
+        #end if
+
+        #if str($strand_type.strand_specific) == "single"
+            -d
+            #if str($strand_type.single_type) == "s"
+                '++,--'
+            #else
+                '+-,-+'
+            #end if
+        #end if
+
+        @MULTIHITS@
+
+        $onlyexonic
+        --single-read="${singleread}"
+        ]]>
+    </command>
+
+    <inputs>
+        <expand macro="bam_param" />
+        <expand macro="refgene_param" />
+        <expand macro="strand_type_param" />
+        <expand macro="multihits_param" />
+        <param name="onlyexonic" type="boolean" value="false" truevalue="--only-exonic" falsevalue="" label="Only use exonic (UTR exons and CDS exons) reads, otherwise use all reads" help="(--only-exonic)"/>
+        <param name="singleread" type="select" label="How should read-pairs that only have one end mapped be counted?" help="(--single-read)">
+            <option value="1" selected="true">Treat it as a whole fragment (1)</option>
+            <option value="0.5">Treat it as a half fragment (0.5)</option>
+            <option value="0">Ignore it (0)</option>
+        </param>
+    </inputs>
+
+    <outputs>
+        <data format="xls" name="outputxls" from_work_dir="output.FPKM.xls"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
+            <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/>
+            <output name="outputxls" file="output.FPKM.xls"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+FPKM_count.py
++++++++++++++
+
+Given a BAM file and reference gene model, this program will calculate the raw
+read count, FPM (fragments per million), and FPKM (fragments per million
+mapped reads per kilobase exon) for each gene in a BED file. For strand
+specific RNA-seq data, program will assign read to its parental gene according
+to strand rule, if you don't know the strand rule, run infer_experiment.py.
+Please note that chromosome ID, genome cooridinates should be concordant
+between BAM and BED files.
+
+Inputs
+++++++++++++++
+
+Input BAM/SAM file
+    Alignment file in BAM/SAM format.
+
+Reference gene model
+    Gene model in BED format.
+
+Strand sequencing type (default=none)
+    See Infer Experiment tool if uncertain.
+
+Options
+++++++++++++++
+
+Skip Multiple Hit Reads
+    Use Multiple hit reads or use only uniquely mapped reads.
+
+Minimum mapping quality
+    Minimum mapping quality (phred scaled) for an alignment to be called
+    "uniquely mapped". default=30
+
+Only use exonic reads
+    Renders program only used exonic (UTR exons and CDS exons) reads,
+    otherwise use all reads.
+
+Single Reads
+    How to count read-pairs that only have one end mapped. 0: ignore it. 0.5:
+    treat it as half fragment. 1: treat it as whole fragment. default=1
+
+Sample Output
+++++++++++++++
+
+======  =========  =========  =========  =========  ===========  ==========  ============  ============
+#chrom  st         end        accession  mRNA_size  gene_strand  Frag_count  FPM           FPKM
+======  =========  =========  =========  =========  ===========  ==========  ============  ============
+chr1    100652477  100715409  NM_001918  10815.0    ‘-‘          5498.0      191.73788949  17.728884835
+chr1    175913961  176176380  NM_022457  2789.0     ‘-‘          923.0       32.188809021  11.541344217
+chr1    150980972  151008189  NM_021222  2977.0     ‘+’          687.0       23.958517657  8.0478729115
+chr1    6281252    6296044    NM_012405  4815.0     ‘-‘          1396.0      48.684265866  10.11095864
+chr1    20959947   20978004   NM_032409  2660.0     ‘+’          509.0       17.750925018  6.6732800821
+chr1    32479294   32509482   NM_006559  2891.0     ‘+’          2151.0      75.014223408  25.947500314
+======  =========  =========  =========  =========  ===========  ==========  ============  ============
+
+@ABOUT@
+
+]]>
+    </help>
+
+    <expand macro="citations" />
+
+</tool>