--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alevin.xml	Mon Sep 09 11:12:51 2019 -0400
@@ -0,0 +1,209 @@
+<tool id="alevin" name="Alevin" version="@VERSION@">
+    <description>Quantification and analysis of 3’ tagged-end single-cell sequencing data</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir ./index
+        && mkdir ./output
+        #if '${refTranscriptSource.TranscriptSource}' != "indexed":
+            && salmon index -i ./index
+                --kmerLen '${refTranscriptSource.s_index.kmer}'
+                --gencode
+                --transcripts '${refTranscriptSource.s_index.fasta}'
+            #set $index_path = './index'
+        #else
+            #set $index_path = $refTranscriptSource.index.fields.path
+        #end if
+        #if $pairstraight.readselect == 'paired':
+            #if $pairstraight.file1.is_of_type("fastq.gz"):
+                && cp '${pairstraight.file1}' ./mate1.fastq.gz
+                && gunzip ./mate1.fastq.gz
+                && cp '${pairstraight.file2}' ./mate2.fastq.gz
+                && gunzip ./mate2.fastq.gz
+            #else if $pairstraight.file1.is_of_type("fastq.bz2"):
+                && cp '${pairstraight.file1}' ./mate1.fastq.bz2
+                && bzip2 -d ./mate1.fastq.bz2
+                && cp '${pairstraight.file2}' ./mate2.fastq.bz2
+                && bzip2 -d ./mate2.fastq.bz2
+            #else:
+                && ln -s '${pairstraight.file1}' ./mate1.fastq
+                && ln -s '${pairstraight.file2}' ./mate2.fastq
+            #end if
+        #else:
+            #if $pairstraight.unmatedreads.is_of_type("fastq.gz"):
+                && cp '${pairstraight.unmatedreads}' ./unmate.fastq.gz
+                && gunzip ./unmate.fastq.gz
+            #else if $pairstraight.unmatedreads.is_of_type("fastq.bz2"):
+                && cp '${pairstraight.unmatedreads}' ./unmate.fastq.bz2
+                && bzip2 -d unmate.fastq.bz2
+            #else:
+                && ln -s '${pairstraight.unmatedreads}' ./unmate.fastq
+            #end if
+        #end if
+
+        && ln -s '${tgmap}' ./alevinmap.tsv
+        && salmon alevin -l
+        #if $pairstraight.readselect == 'paired':
+            ${pairstraight.orientation}${pairstraight.strandedness}
+            -i $index_path
+            -1 ./mate1.fastq
+            -2 ./mate2.fastq
+        #else:
+            '${pairstraight.strandedness}'
+            -i $index_path
+            -r zcat ./unmate.fastq
+        #end if
+        -o ./output
+        -p "\${GALAXY_SLOTS:-4}"
+        ${protocol}
+        --tgMap ./alevinmap.tsv
+        #if $whitelist:
+            --whitelist '${optional.whitelist}'
+        #end if
+        #if $optional.numCellBootstraps:
+            --numCellBootstraps '${optional.numCellBootstraps}'
+        #end if
+        #if $optional.forceCells:
+            --forceCells '${optional.forceCells}'
+        #end if
+        #if $optional.expectCells:
+            --expectCells '${optional.expectCells}'
+        #end if
+        #if $optional.mrna:
+            --mrna '${optional.mrna}'
+        #end if
+        #if $optional.rrna:
+            --rrna '${optional.rrna}'
+        #end if
+        #if $optional.keepCBFraction:
+            --keepCBFraction '${optional.keepCBFraction}'
+        #end if
+        ${optional.dumpBfh}
+        ${optional.dumpFeatures}
+        ${optional.dumpUmiGraph}
+        ${optional.dumpMtx}
+        #if $optional.lowRegionMinNumBarcodes:
+            --lowregionMinNumBarcodes '${optional.lowRegionMinNumBarcodes}'
+        #end if
+        #if $optional.maxNumBarcodes:
+            --maxNumBarcodes '${optional.maxNumBarcodes}'
+        #end if
+        ]]>
+    </command>
+    <inputs>
+        <expand macro="index"/>
+        <conditional name="pairstraight">
+            <param name="readselect" label="Single or paired-end reads?" type="select">
+                <option value="paired">Paired-end</option>
+                <option value="unmated">Single-end</option>
+            </param>
+            <when value="paired">
+                <param name="file1" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" help="CB+UMI raw sequence file(s)"/>
+                <param name="file2" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" help="Read-sequence file(s)"/>
+                <expand macro="orient"/>
+                <expand macro="stranded"/>
+            </when>
+            <when value="unmated">
+                <param name="unmatedreads" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" label="Unmated reads files"/>
+                <expand macro="stranded"/>
+            </when>
+        </conditional>
+        <param name="protocol" type="select">
+            <option value="--dropseq">DropSeq Single Cell protocol</option>
+            <option value="--chromium">10x chromium v2 Single Cell protocol</option>
+            <option value="--chromiumV3">10x chromium v3 Single Cell protocol</option>
+            <option value="--gemcode">Gemcode v1 Single Cell protocol</option>
+            <option value="--celseq">CEL-Seq Single Cell protocol</option>
+            <option value="--celseq2">CEL-Seq2 Single Cell protocol</option>
+        </param>
+        <param name="tgmap" type="data" format="tsv,tabular" label="Transcript to gene map file" help="Tsv with no header, containing two columns mapping each transcript present in the reference to the corresponding gene (the first column is a transcript and the second is the corresponding gene)."/>
+        <param name="allout" type="boolean" label="Retrieve all output files" truevalue="Yes" falsevalue="No" checked="false" help="If not selected, all log, info.txt, and json files output by Alevin will not be retrieved"/>
+        <section name="optional" title="Optional commands" expanded="false">
+            <param name="whitelist" type="data" format="tsv,tabular" optional="true" label="Whitelist file" help="Explicitly specify whitelist CP for cell detection and CB sequence correction. If not specified, putative CBs generated."/>
+            <param name="noDedup" type="boolean" truevalue="Yes" falsevalue="No" checked="false" help="Causes pipeline to only perform CB correction, then maps the read-sequences to the transcriptome generating the interim data-structure of CB-EqClass-UMI-count. Used in parallel with --dumpBarcodeEq or --dumpBfh for the purposes of obtaining raw information or debugging."/>
+            <param name="mrna" type="data" format="tsv" optional="true" help="Single column tsv of mitochondrial genes which are to be used as a feature for CB whitelising naive Bayes classification."/>
+            <param name="rrna" type="data" format="tsv" optional="true" help="Single column tsv of ribosomal genes which are to be used as a feature for CB whitelising naive Bayes classification."/>
+            <param name="dumpBfh" type="boolean" truevalue="--dumpBfh" falsevalue="" checked="false" help="Dumps the full CB-EqClass-UMI-count data-structure for the purposed of allowing raw data analysis and debugging."/>
+            <param name="dumpFeatures" type="boolean" truevalue="--dumpFeatures" falsevalue="" checked="false" help="Dumps all features used by the CB classification and their counts at each cell level. Generally, this is used for the purposes of debugging."/>
+            <param name="dumpUmiGraph" type="boolean" truevalue="--dumpUmiGraph" falsevalue="" checked="false" help="Dump the per-cell level umi graph"/>
+            <param name="dumpMtx" type="boolean" truevalue="--dumpMtx" falsevalue="" checked="false" help="Converts the default binary format of alevin for gene-count matrix into a human readable mtx (matrix market exchange) sparse format."/>
+            <param name="forceCells" type="integer" optional="true" help="Explicitly specify the number of cells."/>
+            <param name="expectCells" type="integer" optional="true" help="define a close upper bound on expected number of cells."/>
+            <param name="numCellBootstraps" type="integer" optional="true" help="Performs certain number of bootstrap and generate the mean and variance of the count matrix"/>
+            <param name="minScoreFraction" type="float" optional="true" help="This value controls the minimum allowed score for a mapping to be considered valid. It matters only when --validateMappings has been passed to Salmon. The maximum possible score for a fragment is ms = read_len * ma (or ms = (left_read_len + right_read_len) * ma for paired-end reads). The argument to --minScoreFraction determines what fraction of the maximum score s a mapping must achieve to be potentially retained. For a minimum score fraction of f, only mappings with a score less than (f * s) will be kept. Mappings with lower scores will be considered as low-quality, and will be discarded."/>
+            <param name="keepCBFraction" type="float" optional="true" help="Fraction of cellular barcodes to keep (Between 0 and 1)."/>
+            <param name="lowRegionMinNumBarcodes" type="integer" optional="true" help="Minimum number of cell barcodes to use fo learning low confidence region (defaults to 200)"/>
+            <param name="maxNumBarcodes" type="integer" optional="true" help="Maximum allowable limit to process the cell barcodes. Defaults to 100000"/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="quants_mat.gz" label="quants_mat.gz" format="txt" from_work_dir="output/alevin/quants_mat.gz">
+            <filter>optional["dumpMtx"] != "Yes"</filter>
+        </data>
+        <data name="quants_mat.mtx.gz" label="quants_mat.mtx.gz" format="mtx" from_work_dir="output/alevin/quants_mat.mtx.gz"/>
+        <data name="quants_mat_cols.txt" label="quants_mat_cols.txt" format="txt" from_work_dir="output/alevin/quants_mat_cols.txt"/>
+        <data name="quants_mat_rows.txt" label="quants_mat_rows.txt" format="txt" from_work_dir="output/alevin/quants_mat_rows.txt"/>
+        <data name="quants_tier_mat.gz" label="quants_tier_mat.gz" format="mtx" from_work_dir="output/alevin/quants_tier_mat.gz"/>
+        <data name="alevin.log" label="alevin.log" format="txt" from_work_dir="output/alevin/alevin.log">
+            <filter>allout</filter>
+        </data>
+        <data name="featureDump.txt" label="featureDump.txt" format="txt" from_work_dir="output/alevin/featureDump.txt"/>
+        <data name="whitelist.txt" label="whitelist.txt" format="txt" from_work_dir="output/alevin/whitelist.txt"/>
+        <data name="bfh.txt" label="bfh.txt" format="txt" from_work_dir="output/alevin/bfh.txt">
+            <filter>optional["dumpBfh"] == "Yes"</filter>
+        </data>
+        <data name="quants_mean_mat.gz" label="quants_mean_mat.gz" format="mtx" from_work_dir="output/alevin/quants_mean_mat.gz">
+            <filter>optional["numCellBootstraps"]</filter>
+        </data>
+        <data name="quants_var_mat.gz" label="quants_var_mat.gz" format="mtx" from_work_dir="output/alevin/quants_var_mat.gz">
+            <filter>optional["numCellBootstraps"]</filter>
+        </data>
+        <data name="quants_boot_rows.txt" label="quants_boot_rows.txt" format="txt" from_work_dir="output/alevin/quants_boot_rows.txt">
+            <filter>optional["numCellBootstraps"]</filter>
+        </data>
+        <data name="alevinmeta_info.json" format="json" label="meta_info.json" from_work_dir="output/aux_info/alevin_meta_info.json">
+            <filter>allout</filter>
+        </data>
+        <data name="ambig_info.tsv" format="tsv" label="ambig_info.tsv" from_work_dir="output/aux_info/ambig_info.tsv">
+            <filter>allout</filter>
+        </data>
+        <data name="meta_info.json" format="json" label="meta_info.json" from_work_dir="output/aux_info/meta_info.json">
+            <filter>allout</filter>
+        </data>
+        <data name="expected_bias.gz" format="txt" label="expected_bias.gz" from_work_dir="output/aux_info/fld.gz"/>
+        <data name="observed_bias.gz" format="txt" label="observed_bias.gz" from_work_dir="output/aux_info/observed_bias.gz"/>
+        <data name="observed_bias_3p.gz" format="txt" label="observed_bias_3p.gz" from_work_dir="output/aux_info/observed_bias_3p.gz"/>
+        <data name="flenDist.txt" format="txt" label="flenDist.txt" from_work_dir="output/libParams/flenDist.txt"/>
+        <data name="salmon_quant.log" format="txt" label="salmon_quant.log" from_work_dir="output/logs/salmon_quant.log">
+            <filter>allout</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="11">
+            <conditional name="refTranscriptSource">
+                <param name="TranscriptSource" value="history"/>
+                <section name="s_index">
+                    <param name="fasta" value="minitranscript.fa"/>
+                </section>
+            </conditional>
+            <conditional name="pairstraight">
+                <param name="readselect" value="paired"/>
+                <param name="file1" value="fastqs/moreminifastq1.fastq.gz"/>
+                <param name="file2" value="fastqs/moreminifastq2.fastq.gz"/>
+                <param name="orientation" value="I"/>
+                <param name="strandedness" value="SR"/>
+            </conditional>
+            <param name="protocol" value="--chromium"/>
+            <param name="tgmap" value="minitxp.tsv"/>
+            <param name="dumpMtx" value="Yes"/>
+            <output name="quants_mat.mtx.gz" file="alevin_mat.mtx.gz" ftype="mtx" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        @salmonhelp@
+        @alevinhelp@
+    ]]></help>
+    <expand macro="citations"/>
+</tool>