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1 <tool id="monorail" name="Run the Monorail RNA-seq analysis pipeline" version="0.1.0">
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15
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2 <!-- much of this was based on https://github.com/galaxyproject/tools-iuc/blob/master/tools/rgrnastar/rg_rnaStar.xml -->
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1
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3 <requirements>
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4 <requirement type="package" version="1.9">samtools</requirement>
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17
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5 <requirement type="package" version="2.7.3a">star</requirement>
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32
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6 <requirement type="package" version="0.4.0">bamcount</requirement>
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16
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7 <requirement type="package" version="5.4.0">snakemake-minimal</requirement>
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8 <requirement type="package" version="1.3.3">zstd</requirement>
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9 <requirement type="package" version="1.3">seqtk</requirement>
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10 <!--
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11 <requirement type="package" version="2.1.0">hisat2</requirement>
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12 <requirement type="package" version="0.8">fastq-tools</requirement>
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13 <requirement type="package" version="0.12.0">salmon</requirement>
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14 <requirement type="package" version="0.5.0">regtools</requirement>
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15 <requirement type="package" version="2.9.1">sra-tools</requirement>
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16 -->
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1
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17 </requirements>
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18 <!-- /bin/bash -x monorail.slim.sh ../ath10 4 10 ../ath10/gtf/exons.bed ./tmp2 ../fastqs/SRR8505407_1_100.fastq.gz ../fastqs/SRR8505407_2_100.fastq.gz -->
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8
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19 <command detect_errors="aggressive"><![CDATA[
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20 run_mr_snakemake.sh "$__tool_directory__/Snakefile"
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21 \${GALAXY_SLOTS:-4}
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22 "$index_source.fields.path"
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23 "$index_source.fields.path/$index_source.fields.name/gtf/exons.bed"
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24 "."
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25 "./tmp"
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26 "$index_source.fields.name"
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1
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27 #if str($singlePaired.sPaired) == "paired_collection"
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37
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28 "$singlePaired.input.forward,$singlePaired.input.reverse"
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15
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29 #if $singlePaired.input.forward.is_of_type("fastq.gz"):
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37
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30 "compressed=1"
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15
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31 #end if
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1
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32 #else
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37
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33 "$singlePaired.input1"
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34 #if str($singlePaired.sPaired) == "paired"
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8
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35 inputs="$singlePaired.input1,$singlePaired.input2"
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1
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36 #end if
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15
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37 #if $singlePaired.input1.is_of_type("fastq.gz"):
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37
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38 "compressed=1"
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15
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39 #end if
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1
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40 #end if
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41 ]]></command>
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23
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42 <inputs>
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1
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43 <!-- FASTQ input(s) and options specifically for paired-end data. -->
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44 <conditional name="singlePaired">
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45 <param name="sPaired" type="select" label="Single-end or paired-end reads">
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46 <option value="single" selected="true">Single-end</option>
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47 <option value="paired">Paired-end (as individual datasets)</option>
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48 <option value="paired_collection">Paired-end (as collection)</option>
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49 </param>
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50 <when value="single">
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51 <param format="fastq,fastq.gz" name="input1" type="data" label="RNA-Seq FASTQ file"/>
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52 </when>
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53 <when value="paired">
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54 <param format="fastq,fastq.gz" name="input1" type="data" label="RNA-Seq FASTQ file, forward reads"/>
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55 <param format="fastq,fastq.gz" name="input2" type="data" label="RNA-Seq FASTQ file, reverse reads"/>
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56 </when>
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57 <when value="paired_collection">
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58 <param format="fastq,fastq.gz" name="input" type="data_collection" collection_type="paired" label="RNA-Seq FASTQ paired reads"/>
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59 </when>
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60 </conditional>
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61
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62 <!--
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63 <param name="refGenomeSource" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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64 <options from_data_table="rnastar_index2">
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65 <filter type="static_value" column="4" value="0"/>
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66 <filter type="sort_by" column="2" />
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67 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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68 </options>
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69 </param>
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70 -->
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71
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72 <!-- Genome source. -->
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24
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73 <param name="index_source" type="select" label="Select reference genome index set" help="If your genome of interest is not listed, contact the Galaxy team">
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26
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74 <options from_data_table="monorail_index">
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75 <filter type="sort_by" column="2" />
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76 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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77 </options>
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78 </param>
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23
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79 </inputs>
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8
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80 <outputs>
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81 <data format="txt" name="auc" label="${tool.name} on ${on_string}: AUC" from_work_dir="bamcount_auc.tsv"/>
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35
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82 <data format="interval" name="splice_junctions" label="${tool.name} on ${on_string}: splice junctions" from_work_dir="SJ.out.tab"/>
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83 <!--
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84 <data format="txt" name="frag" label="${tool.name} on ${on_string}: Fragment Distribution" from_work_dir="bamcount_frag.tsv"/>
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6
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85 <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out"/>
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7
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86 <data format="txt" name="auc" label="${tool.name} on ${on_string}: AUC" from_work_dir="bc.auc.tsv"/>
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87 <data format="txt" name="bc_log" label="${tool.name} on ${on_string}: bamcount log" from_work_dir="bc.log"/>
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6
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88 <data format="interval" name="chimeric_junctions" label="${tool.name} on ${on_string}: chimeric junctions" from_work_dir="Chimeric.out.junction"/>
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89 <data name="mapped_reads" format="bam" label="${tool.name} on ${on_string}: mapped.bam" from_work_dir="sorted.bam"/>
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90 <data name="mapped_reads_index" format="bai" label="${tool.name} on ${on_string}: mapped.bam.bai" from_work_dir="sorted.bam.bai"/>
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91 -->
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92 </outputs>
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93 <help>
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94 Run the Monorail RNA-seq analysis pipeline
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95 </help>
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96 </tool>
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