--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scpipe.xml	Wed Aug 15 13:54:40 2018 -0400
@@ -0,0 +1,264 @@
+<tool id="scpipe" name="scPipe" version="1.0.0">
+    <description>- preprocessing pipeline for single cell RNA-seq</description>
+    <requirements>
+        <requirement type="package" version="1.0.0">bioconductor-scpipe</requirement>
+        <requirement type="package" version="1.28.1">bioconductor-rsubread</requirement>
+        <requirement type="package" version="1.20">r-knitr</requirement>
+        <requirement type="package" version="1.10">r-rmarkdown</requirement>
+        <requirement type="package" version="1.1.1">r-readr</requirement>
+        <requirement type="package" version="4.7.1">r-plotly</requirement>
+        <requirement type="package" version="0.4">r-dt</requirement>
+        <requirement type="package" version="1.6.0">bioconductor-scater</requirement>
+        <requirement type="package" version="1.6.2">bioconductor-scran</requirement>
+        <requirement type="package" version="0.13">r-rtsne</requirement>
+        <!-- Using older version of ggplot2 as getting error like this with 3.0.0: 
+        https://github.com/ggobi/ggally/issues/263  -->
+        <requirement type="package" version="2.2.1">r-ggplot2</requirement>      
+        <requirement type="package" version="1.6.0">r-optparse</requirement>
+    </requirements>
+    <version_command><![CDATA[
+echo $(R --version | grep version | grep -v GNU)", scPipe version" $(R --vanilla --slave -e "library(scPipe); cat(sessionInfo()\$otherPkgs\$scPipe\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", Rsubread version" $(R --vanilla --slave -e "library(Rsubread); cat(sessionInfo()\$otherPkgs\$Rsubread\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", knitr version" $(R --vanilla --slave -e "library(knitr); cat(sessionInfo()\$otherPkgs\$knitr\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rmarkdown version" $(R --vanilla --slave -e "library(rmarkdown); cat(sessionInfo()\$otherPkgs\$rmarkdown\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", readr version" $(R --vanilla --slave -e "library(readr); cat(sessionInfo()\$otherPkgs\$readr\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", plotly version" $(R --vanilla --slave -e "library(plotly); cat(sessionInfo()\$otherPkgs\$plotly\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", DT version" $(R --vanilla --slave -e "library(DT); cat(sessionInfo()\$otherPkgs\$DT\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scater version" $(R --vanilla --slave -e "library(scater); cat(sessionInfo()\$otherPkgs\$scater\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scran version" $(R --vanilla --slave -e "library(scran); cat(sessionInfo()\$otherPkgs\$scran\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rtsne version" $(R --vanilla --slave -e "library(Rtsne); cat(sessionInfo()\$otherPkgs\$Rtsne\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", ggplot2 version" $(R --vanilla --slave -e "library(ggplot2); cat(sessionInfo()\$otherPkgs\$ggplot2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
+    ]]></version_command>
+    <command detect_errors="exit_code"><![CDATA[
+#import re
+
+## Link input files
+
+#if $ref_fasta.fasta_source == "history":
+    #set $fasta_name = re.sub('[^\w\-\s]', '_', str($ref_fasta.ref_fa_hist.element_identifier))
+    ln -s '$ref_fasta.ref_fa_hist' '$fasta_name' &&
+#else:
+    #set $fasta_name = re.sub('[^\w\-\s]', '_', str($ref_fasta.ref_fa_builtin.element_identifier))
+    ln -s '$ref_fasta.ref_fa_builtin.fields.path' '$fasta_name' &&
+#end if
+
+#set $anno_name = re.sub('[^\w\-\s]', '_', str($exons.element_identifier))
+#set $anno_name = $anno_name + ".gff3"
+ln -s '${exons}' '$anno_name' &&
+
+#if $paired_format.paired_format_selector == 'paired_collection':
+    #set $in1 = $paired_format.paired_input.forward
+    #set $in2 = $paired_format.paired_input.reverse
+    #set $in1_name = re.sub('[^\w\-\s]', '_', str($paired_format.paired_input.name))
+    #set $in2_name = re.sub('[^\w\-\s]', '_', str("%s_%s" % ($paired_format.paired_input.name, "R2")))
+    #set out1 = $output_paired_coll.forward
+    #set out2 = $output_paired_coll.reverse
+    ln -s '$in1' '$in1_name' &&
+    ln -s '$in2' '$in2_name' &&
+#else
+    #set $in1_name = re.sub('[^\w\-\s]', '_', str($in1.element_identifier))
+    ln -s '$in1' '$in1_name' &&
+
+    #if str($paired_format.paired_format_selector) == 'paired':
+        #set $in2_name = re.sub('[^\w\-\s]', '_', str($in2.element_identifier))
+        ln -s '$in2' '$in2_name' &&
+    #end if
+#end if
+
+#if $rscript:
+    cp '$__tool_directory__/scpipe.R' '$out_rscript' &&
+#end if
+
+TAB=\$(printf '\t') &&
+
+#if $barcodes:
+    sed -i.bak -e "s/\${TAB}/,/g" '$barcodes' &&
+#end if
+
+## Run scPipe
+
+Rscript '$__tool_directory__/scpipe.R'
+
+--fasta '$fasta_name'
+--exons '$anno_name'
+--samplename '$in1_name'
+--read1 '$in1_name'
+--read2 '$in2_name'
+--bs1 $bs1
+--bl1 $bl1
+--bs2 $bs2
+--bl2 $bl2
+--us $us
+--ul $ul
+
+#if $barcodes:
+    --barcodes '$barcodes'
+#end if
+
+#if $report:
+    --report '$report'
+#end if
+
+#if $rdata:
+    --rdata '$rdata'
+#end if
+
+--rmlow $adv.rmlow
+--rmN $adv.rmN
+--minq $adv.minq
+--numbq $adv.numbq
+--stnd $adv.stnd
+--max_mis $adv.max_mis
+--UMI_cor $adv.UMI_cor
+--gene_fl $adv.gene_fl
+--max_reads $adv.max_reads
+--min_count $adv.min_count
+--nthreads \${GALAXY_SLOTS:-2}
+
+&&
+sed -e "s/,/\${TAB}/g" gene_count.csv > gene_count.tsv
+
+]]></command>
+
+    <inputs>
+        <conditional name="ref_fasta">
+            <param name="fasta_source" type="select" label="Reference genome FASTA">
+                <option value="cached" selected="true">Use a built-in genome</option>
+                <option value="history">Use a FASTA from history</option>
+            </param>
+            <when value="cached">
+                <param name="ref_fa_builtin" type="select" label="Select a built-in FASTA" help="If your genome of interest is not listed, contact your Galaxy administrator">
+                    <options from_data_table="all_fasta">
+                        <filter type="sort_by" column="2" />
+                        <validator type="no_options" message="No FASTA is available for the selected input dataset" />
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param name="ref_fa_hist" type="data" format="fasta" label="Select a history FASTA" />
+            </when>
+        </conditional>
+        <param name="exons" type="data" format="gff3" label="Exon annotation GFF3 file" help="Current supported sources: ENSEMBL, GENCODE and RefSeq"/>
+
+        <conditional name="paired_format">
+            <param name="paired_format_selector" type="select" label="Paired reads or Paired collection">
+                <option value="paired">Paired</option>
+                <option value="paired_collection">Paired Collection</option>
+            </param>
+            <when value="paired">
+                <param name="in1" type="data" format="fastq.gz,fastq" label="Input Read 1" help="Read 1 should contain the transcripts in fastq.gz format"/>
+                <param name="in2" type="data" format="fastq.gz,fastq" label="Input Read 2" help="Read 2 should contain UMI and barcodes in fastq.gz format"/>
+            </when>
+            <when value="paired_collection">
+                <param name="paired_input" type="data_collection" collection_type="paired" format="fastq.gz,fastq" label="Select paired collection(s)"/>
+            </when>
+        </conditional>
+        <param name="barcodes" type="data" format="tabular,tsv" optional="True" label="Cell barcodes file" help="Optional file of cell barcodes. Should contain at least two columns, where the first column has the cell id and the second column contains the barcode sequence."/>
+        <param argument="--bs1" type="integer" min="-1" value="-1" label="Barcode start Read 1" help="Barcode start position in Read 1. Positions are 0-indexed so the first base is considered base 0, -1 indicates no barcode. Default: -1" />
+        <param argument="--bl1" type="integer" min="0" value="0" label="Barcode length Read 1" help="Barcode length in Read 1, 0 if no barcode present. Default: 0" />
+        <param argument="--bs2" type="integer" min="-1" value="6" label="Barcode start Read 2" help="Barcode start position in Read 2. Positions are 0-indexed so the first base is considered base 0, -1 indicates no barcode.  Default: 6" />
+        <param argument="--bl2" type="integer" min="0" value="8" label="Barcode length Read 2" help="Barcode length in Read 2, 0 if no barcode present. Default: 8" />
+        <param argument="--us" type="integer" min="-1" value="0" label="UMI start Read 2" help="UMI start position in Read 2. Positions are 0-indexed so the first base is considered base 0, -1 indicates no UMI.  Default: 0" />
+        <param argument="--ul" type="integer" min="0" value="6" label="UMI length Read 2" help="UMI length in Read 2, 0 if no UMI present. Default: 6" />
+        <param name="report" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Output HTML Report?" help="If this option is set to Yes, a HTML report containing QC metrics will be output. Default: Yes" />
+        <param name="rscript" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used to annotate the IDs will be provided as a text file in the output. Default: No" />
+        <param name="rdata" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output RData file?"
+            help="Output all the data used by R to construct the tables and plots, can be loaded into R. Default: No">
+        </param>
+        <section name="adv" title="Advanced Options">
+            <param argument="--rmlow" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Remove reads with N in barcode or UMI. Default: Yes" />
+            <param argument="--rmN" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Remove reads with low quality. Default: Yes" />
+            <param argument="--minq" type="integer" min="0" value="20" label="Minimum read quality. Default: 20" />
+            <param argument="--numbq" type="integer" min="0" value="2" label="Maximum number of bases below minq. Default: 2" />
+            <param argument="--stnd" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Perform strand-specific mapping. Default: Yes" />
+            <param argument="--max_mis" type="integer" min="0" value="1" label="Maximum mismatch allowed in barcode. Default: 1" />
+            <param argument="--UMI_cor" type="integer" min="0" value="1" label="Correct UMI sequence error" help="0 means no correction, 1 means simple correction and merge UMI with distance 1. Default: 1" />
+            <param argument="--gene_fl" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Remove low abundant genes" help="Low abundant is defined as only one copy of one UMI for this gene. Default: No" />
+            <param argument="--max_reads" type="integer" min="0" value="1000000" label="Maximum reads processed" help="Maximum reads processed if detecting barcodes. Default: 1,000,000" />
+            <param argument="--min_count" type="integer" min="0" value="10" label="Minimum count to keep" help="Minimum count to keep if detecting barcodes. Barcode will be discarded if it has lower count. This should be set according to --max_reads. Default: 10" />
+        </section>
+    </inputs>
+
+    <outputs>
+        <data name="out_matrix" format="tabular" from_work_dir="gene_count.tsv" label="${tool.name} on ${on_string}: Count Matrix" />
+        <data name="out_report" format="html" from_work_dir="report.nb.html" label="${tool.name} on ${on_string}: HTML Report" >
+            <filter>report</filter>
+        </data>
+        <data name="out_rscript" format="txt" from_work_dir="out_rscript.txt" label="${tool.name} on ${on_string}: Rscript">
+            <filter>rscript</filter>
+        </data>
+        <data name="out_rdata" format="rdata" from_work_dir="scPipe_analysis.RData" label="${tool.name} on ${on_string}: RData file">
+            <filter>rdata</filter>
+        </data>
+    </outputs>
+
+    <tests>
+        <!-- Ensure outputs work -->
+        <test>
+            <param name="fasta_source" value="history"/>
+            <param name="ref_fa_hist" ftype="fasta" value="mm10_MT19.fa.gz"/>
+            <param name="exons" ftype="gff3" value="mm10_MT19.gff3.gz"/>
+            <param name="paired_format_selector" value="paired" />
+            <param name="in1" ftype="fastqsanger.gz" value="CB51_MT19_R1.gz"/>
+            <param name="in2" ftype="fastqsanger.gz" value="CB51_MT19_R2.gz"/>
+            <param name="us" value="-1"/>
+            <param name="max_reads" value="5000000"/>
+            <param name="min_count" value="100"/>
+            <param name="report" value="True" />
+            <output name="out_matrix" >
+                <assert_contents>
+                    <has_text text="ENSMUSG00000024940" />
+                </assert_contents>
+            </output>
+            <output name="out_report" >
+                <assert_contents>
+                    <has_text text="scPipe report for sample" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+scPipe_ is an `R/Bioconductor package`_ that integrates barcode demultiplexing, read alignment, UMI-aware gene-level quantification and quality control of raw sequencing data generated by multiple protocols that include CEL-seq, MARS-seq, Chromium 10X, Drop-seq and Smart-seq. scPipe produces a count matrix that is essential for downstream analysis along with an HTML report that summarises data quality. These results can be used as input for downstream analyses including normalization, visualization and statistical testing. 
+Examples of the report output can be found here_.
+
+-----
+
+**Inputs**
+
+    * Reference genome in FASTA format
+    * Exon annotation in GFF3 format
+    * Paired-end FASTQ.GZ reads
+    * Cell barcodes TAB-separated file (Optional)
+
+*Read Structure*
+
+The default read structure represents CEL-seq
+paired-ended reads, with one cell barcode in Read 2 Start from
+6bp and UMI sequence in Read 2 Start from the first bp. So the
+read structure will be : `bs1=-1, bl1=0, bs2=6, bl2=8, us=0,
+ul=6`. `bs1=-1, bl1=0` means we don't have index in Read 1 so we
+set a negative value to start position and zero to the length.
+`bs2=6, bl2=8` means we have index in Read 2 which starts at 6bp
+with 8bp length. `us=0, ul=6` means we have UMI from the
+start of Read 2 and the length is 6bp. NOTE: the zero
+based index is used so the index of the sequence starts from zero. For a
+typical Drop-seq experiment the setting will be `bs1=-1,
+bl1=0, bs2=0, bl2=12, us=12, ul=8`, which means Read 1 only
+contains transcript and the first 12bp in Read 2 are index,
+followed by 8bp UMIs.
+
+-----
+
+**Outputs**
+
+    * Count matrix of genes in Tabular format
+
+Optionally you can choose to output
+
+    * HTML report (default is Yes)
+    * Rscript
+    * RData
+
+.. _scPipe: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006361
+.. _R/Bioconductor package: https://bioconductor.org/packages/release/bioc/html/scPipe.html
+.. _here: http://bioinf.wehi.edu.au/scPipe/
+
+]]></help>
+    <citations>
+        <citation type="doi">10.1371/journal.pcbi.1006361</citation>
+    </citations>
+</tool>