--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kallisto_pseudo.xml	Tue Aug 22 04:16:08 2017 -0400
@@ -0,0 +1,224 @@
+<?xml version="1.0"?>
+<tool id="kallisto_pseudo" name="Kallisto pseudo" version="@VERSION@.0">
+    <description>- run pseudoalignment on RNA-Seq transcripts</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code">
+        <![CDATA[
+        #if $reference_genome.reference_genome_source == "history":
+            ln -s '$reference_genome.reference' reference.fa &&
+            kallisto index reference.fa -i reference.kallisto &&
+            #set index_path = 'reference.kallisto'
+        #else:
+            #set index_path = $reference_genome.index.fields.path
+        #end if
+        kallisto pseudo -i '$index_path'
+            #if $pseudobam:
+                $pseudobam -o .
+            #else:
+                --threads \${GALAXY_SLOTS:-1}
+                -o .
+            #end if
+
+
+            #if str($single_paired.single_paired_selector) == 'single':
+                --single --fragment-length $single_paired.fragment_length
+                --sd $single_paired.sd '$single_paired.reads'
+            #else:
+                #if str($single_paired.collection.collection_selector) == 'collection':
+                    '$single_paired.collection.reads.forward'
+                    '$single_paired.collection.reads.reverse'
+                #else:
+                    #if str($single_paired.collection.fastq_umi.umi) == 'yes':
+                        --batch '$batch' --umi
+                    #else:
+                        '$single_paired.collection.fastq_umi.forward'
+                        '$single_paired.collection.fastq_umi.reverse'
+                    #end if
+                #end if
+            #end if
+            #if $pseudobam:
+                | samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -o '$pseudobam_output' -
+            #end if
+            && if [ -f run_info.json ] ; then cat run_info.json ; fi &&
+            mkdir outputs &&
+            if [ -f matrix.ec ] ; then mv matrix.ec outputs/Matrix.ec ; fi &&
+            if [ -f matrix.tsv ] ; then mv matrix.tsv outputs/Matrix.tabular ; fi &&
+            if [ -f matrix.cells ] ; then mv matrix.cells outputs/Matrix.cells ; fi &&
+            if [ -f pseudoalignments.tsv ] ; then mv pseudoalignments.tsv outputs/Pseudoalignments.tabular ; fi &&
+            if [ -f pseudoalignments.ec ] ; then mv pseudoalignments.ec outputs/Pseudoalignments.ec ; fi
+        ]]>
+    </command>
+    <configfiles>
+        <configfile name="batch">
+<![CDATA[
+#if str($single_paired.single_paired_selector) == 'single':
+cell1	$single_paired.reads
+#else:
+#if str($single_paired.collection.collection_selector) == 'collection':
+cell1	$single_paired.collection.reads.forward $single_paired.collection.reads.reverse
+#else:
+cell1	$single_paired.collection.fastq_umi.forward $single_paired.collection.fastq_umi.reverse
+#end if
+#end if
+]]>
+        </configfile>
+    </configfiles>
+    <inputs>
+        <conditional name="reference_genome">
+            <param name="reference_genome_source" type="select" label="Reference genome for pseudoalignment">
+                <option value="indexed" selected="true">Use a built-in genome</option>
+                <option value="history">Use a genome from history</option>
+            </param>
+            <when value="indexed">
+                <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy administrator">
+                    <options from_data_table="kallisto_indexes">
+                        <filter type="sort_by" column="2" />
+                        <validator type="no_options" message="No genomes are available for the selected input dataset" />
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param name="reference" type="data" format="fasta" label="FASTA reference genome" />
+            </when>
+        </conditional>
+        <conditional name="single_paired">
+            <param name="single_paired_selector" type="select" label="Single-end or paired reads">
+                <option value="single" selected="true">Single-end</option>
+                <option value="paired">Paired</option>
+            </param>
+            <when value="single">
+                <param name="reads" type="data" format="fastq" multiple="True" label="Reads in FASTQ format" />
+                <param name="fragment_length" argument="--fragment-length" type="integer" value="200" label="Average fragment length" />
+                <param argument="--sd" type="integer" value="20" label="Estimated standard deviation of fragment length" />
+            </when>
+            <when value="paired">
+                <conditional name="collection">
+                    <param name="collection_selector" type="select" label="Collection or individual datasets">
+                        <option value="datasets" selected="true">Individual files</option>
+                        <option value="collection">Pair or list of pairs</option>
+                    </param>
+                    <when value="datasets">
+                        <conditional name="fastq_umi">
+                            <param name="umi" type="select" label="Pseudoalignment uses UMIs">
+                                <option value="no" selected="true">Paired FASTQ</option>
+                                <option value="yes">UMI</option>
+                            </param>
+                            <when value="yes">
+                                <param name="forward" type="data" format="tabular" multiple="True" label="UMI file" />
+                                <param name="reverse" type="data" format="fastq" multiple="True" label="FASTQ reads" />
+                            </when>
+                            <when value="no">
+                                <param name="forward" type="data" format="fastq" multiple="True" label="Forward reads" />
+                                <param name="reverse" type="data" format="fastq" multiple="True" label="Reverse reads" />
+                            </when>
+                        </conditional>
+                    </when>
+                    <when value="collection">
+                        <param name="reads" type="data_collection" format="fastq" collection_type="paired" label="Collection of reads" />
+                    </when>
+                </conditional>
+            </when>
+        </conditional>
+        <param argument="--pseudobam" type="boolean" truevalue="--pseudobam" falsevalue="" label="Output pseudoalignments in BAM format" />
+    </inputs>
+    <outputs>
+        <data format="tabular" name="sample">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="outputs" ext="tabular" visible="true" />
+        </data>
+        <data format="bam" name="pseudobam_output" label="${tool.name} on ${on_string}: Pseudoalignments (BAM)">
+            <filter>pseudobam</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="reference_genome_source" value="history" />
+            <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
+            <param name="single_paired_selector" value="paired" />
+            <param name="collection_selector" value="datasets" />
+            <param name="umi" value="yes" />
+            <param name="forward" ftype="tabular" value="mm10_chrM.umi" />
+            <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq" />
+            <output name="sample">
+                <discovered_dataset designation="Matrix.tabular" file="kallisto_pseudo_out1.tab" ftype="tabular" />
+                <discovered_dataset designation="Matrix.ec" file="kallisto_pseudo_out1.ec" ftype="tabular" />
+                <discovered_dataset designation="Matrix.cells" file="kallisto_pseudo_out1.cells" ftype="tabular" />
+            </output>
+        </test>
+        <test>
+            <param name="reference_genome_source" value="history" />
+            <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
+            <param name="single_paired_selector" value="paired" />
+            <param name="collection_selector" value="collection" />
+            <param name="umi" value="no" />
+            <param name="reads">
+                <collection type="paired">
+                    <element name="forward" value="mm10_chrM-1.f.fq" />
+                    <element name="reverse" value="mm10_chrM-1.r.fq" />
+                </collection>
+            </param>
+            <output name="sample">
+                <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out2.tab" ftype="tabular" />
+                <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out2.ec" ftype="tabular" />
+            </output>
+        </test>
+        <test>
+            <param name="reference_genome_source" value="history" />
+            <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
+            <param name="single_paired_selector" value="single" />
+            <param name="collection_selector" value="collection" />
+            <param name="reads" ftype="fastq" value="mm10_chrM-1.f.fq" />
+            <output name="sample">
+                <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out3.tab" ftype="tabular" />
+                <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out3.ec" ftype="tabular" />
+            </output>
+        </test>
+        <test>
+            <param name="reference_genome_source" value="history" />
+            <param name="reference" ftype="fasta" value="felCat8_chrM.fa" />
+            <param name="single_paired_selector" value="paired" />
+            <param name="collection_selector" value="datasets" />
+            <param name="umi" value="no" />
+            <param name="forward" ftype="fastq" value="felCat8_chrM_F.fq" />
+            <param name="reverse" ftype="fastq" value="felCat8_chrM_R.fq" />
+            <output name="sample">
+                <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out4.tab" ftype="tabular" />
+                <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out4.ec" ftype="tabular" />
+            </output>
+        </test>
+        <test>
+            <param name="reference_genome_source" value="cached" />
+            <param name="single_paired_selector" value="paired" />
+            <param name="collection_selector" value="datasets" />
+            <param name="pseudobam" value="true" />
+            <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_F.fq.gz" />
+            <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" />
+            <output name="sample">
+                <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out5.tab" ftype="tabular" />
+                <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out5.ec" ftype="tabular" />
+            </output>
+            <output name="pseudobam_output" file="kallisto_pseudo_out5.bam" ftype="bam" />
+        </test>
+        <test>
+            <param name="reference_genome_source" value="cached" />
+            <param name="single_paired_selector" value="paired" />
+            <param name="collection_selector" value="datasets" />
+            <param name="umi" value="yes" />
+            <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM.umi" />
+            <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" />
+            <output name="sample">
+                <discovered_dataset designation="Matrix.tabular" file="kallisto_pseudo_out6.tab" ftype="tabular" />
+                <discovered_dataset designation="Matrix.ec" file="kallisto_pseudo_out6.ec" ftype="tabular" />
+                <discovered_dataset designation="Matrix.cells" file="kallisto_pseudo_out6.cells" ftype="tabular" />
+            </output>
+        </test>
+    </tests>
+    <help>
+ <![CDATA[
+ `kallisto <https://pachterlab.github.io/kallisto/manual>`__ is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.
+ ]]>
+     </help>
+    <expand macro="citations" />
+</tool>