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1 <tool id="monorail" name="Run the Monorail RNA-seq analysis pipeline" version="0.1.0">
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2 <requirements>
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3 <requirement type="package" version="1.9">samtools</requirement>
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4 <requirement type="package" version="2.6.0b">star</requirement>
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5
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5 <requirement type="package" version="0.2.6">bamcount</requirement>
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6 <!-- <requirement type="package" version="5.4.0">snakemake-minimal</requirement> -->
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7 </requirements>
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8 <!-- /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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9 <command detect_errors="aggressive"><![CDATA[
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10 /bin/bash -x "$__tool_directory__/monorail.sh"
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11 $refGenomeSource.GTFconditional.genomeDir.fields.path
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12 \${GALAXY_SLOTS:-4}
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13 $min_uniq_qual
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14 $exons
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15 ./
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16 #if str($singlePaired.sPaired) == "paired_collection"
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17 '$singlePaired.input.forward' '$singlePaired.input.reverse'
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18 #else
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19 '$singlePaired.input1'
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20 #if str($singlePaired.sPaired) == "paired"
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21 '$singlePaired.input2'
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22 #end if
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23 #end if
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24 ]]></command>
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25 <inputs>
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26 <!-- FASTQ input(s) and options specifically for paired-end data. -->
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27 <conditional name="singlePaired">
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28 <param name="sPaired" type="select" label="Single-end or paired-end reads">
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29 <option value="single" selected="true">Single-end</option>
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30 <option value="paired">Paired-end (as individual datasets)</option>
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31 <option value="paired_collection">Paired-end (as collection)</option>
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32 </param>
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33 <when value="single">
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34 <param format="fastq,fastq.gz" name="input1" type="data" label="RNA-Seq FASTQ file"/>
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35 </when>
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36 <when value="paired">
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37 <param format="fastq,fastq.gz" name="input1" type="data" label="RNA-Seq FASTQ file, forward reads"/>
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38 <param format="fastq,fastq.gz" name="input2" type="data" label="RNA-Seq FASTQ file, reverse reads"/>
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39 </when>
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40 <when value="paired_collection">
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41 <param format="fastq,fastq.gz" name="input" type="data_collection" collection_type="paired" label="RNA-Seq FASTQ paired reads"/>
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42 </when>
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43 </conditional>
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44
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45 <!--
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46 <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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47 <options from_data_table="rnastar_index2">
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48 <filter type="static_value" column="4" value="0"/>
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49 <filter type="sort_by" column="2" />
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50 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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51 </options>
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52 </param>
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53 -->
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54
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55 <!-- Genome source. -->
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56 <conditional name="refGenomeSource">
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57 <param name="geneSource" type="select" label="Custom or built-in reference genome" help="Built-ins were indexed using default options">
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58 <option value="indexed" selected="True">Use a built-in index</option>
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59 <option value="history">Use reference genome from history and create temporary index</option>
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60 </param>
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61 <when value="indexed">
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62 <conditional name="GTFconditional">
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63 <param name="GTFselect" type="select" label="Reference genome with or without an annotation" help="Must the index have been created WITH a GTF file (if not you can specify one afterward).">
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64 <option value="without-gtf">use genome reference without builtin gene-model</option>
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65 <option value="with-gtf">use genome reference with builtin gene-model</option>
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66 </param>
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67 <when value="with-gtf">
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68 <param name="genomeDir" argument="--genomeDir" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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69 <options from_data_table="rnastar_index2">
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70 <filter type="static_value" column="4" value="1"/>
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71 <filter type="sort_by" column="2" />
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72 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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73 </options>
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74 </param>
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75 </when>
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76 <when value="without-gtf">
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77 <param name="genomeDir" argument="--genomeDir" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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78 <options from_data_table="rnastar_index2">
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79 <filter type="static_value" column="4" value="0"/>
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80 <filter type="sort_by" column="2" />
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81 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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82 </options>
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83 </param>
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84 </when>
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85 </conditional>
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86 </when>
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87 <when value="history">
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88 <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />
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89 </when>
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90 </conditional>
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91
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92 <param name="exons" type="data" format="bed" label="Exon annotation BED file" help="Upload/use a BED formatted list of exon intervals for quantifying"/>
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93 <!-- <param name="exon_annotation" type="select" label="Select an exon annotation BED file" help="If your exon annotation is not listed, contact the Galaxy team">
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94 <options from_data_table="exon_annotations">
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95 <filter type="static_value" column="4" value="0"/>
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96 <filter type="sort_by" column="2" />
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97 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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98 </options>
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99 </param> -->
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100 <param name="min_uniq_qual" type="integer" value="10" label="Minimum mapping quality for unique alignments" help="Set this to an appropriate integer value to filter out non-unique alignments"/>
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101 </inputs>
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102
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103
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104 <!-- <expand macro="dbKeyActions" /> -->
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105 <outputs>
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106 <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out">
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107 </data>
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108 <data format="interval" name="chimeric_junctions" label="${tool.name} on ${on_string}: chimeric junctions" from_work_dir="Chimeric.out.junction">
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109 </data>
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110
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111 <data format="interval" name="splice_junctions" label="${tool.name} on ${on_string}: splice junctions.bed" from_work_dir="SJ.out.tab">
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112 </data>
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113 <data name="mapped_reads" format="bam" label="${tool.name} on ${on_string}: mapped.bam" from_work_dir="sorted.bam">
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114 </data>
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115 <data name="mapped_reads_index" format="bai" label="${tool.name} on ${on_string}: mapped.bam.bai" from_work_dir="sorted.bam.bai">
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116 </data>
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117 </outputs>
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118 <help>
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119 Run the Monorail RNA-seq analysis pipeline
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120 </help>
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121 </tool>
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