Mercurial > repos > iuc > kallisto_quant

annotate kallisto_quant.xml @ 2:798ea2ebfc41 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
author iuc
date Tue, 22 Aug 2017 04:14:22 -0400
parents 7f698e0094e5
children da068c8ea6d8
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16c923816e87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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1 <?xml version="1.0"?>
1
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2 <tool id="kallisto_quant" name="Kallisto quant" version="@VERSION@.1">
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3 <description>- quantify abundances of RNA-Seq transcripts</description>
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4 <macros>
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5 <import>macros.xml</import>
16c923816e87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code">
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9 <![CDATA[
16c923816e87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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10 #if $reference_genome.reference_genome_source == "history":
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11 ln -s '$reference_genome.reference' reference.fa &&
16c923816e87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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12 kallisto index reference.fa -i reference.kallisto &&
16c923816e87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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13 #set index_path = 'reference.kallisto'
16c923816e87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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14 #else:
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15 #set index_path = $reference_genome.index.fields.path
16c923816e87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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16 #end if
16c923816e87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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17 kallisto quant -i '$index_path'
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18 $bias --bootstrap-samples $bootstrap_samples --seed $seed $fusion $pseudobam
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19 #if $pseudobam:
16c923816e87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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20 -o .
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21 #else:
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22 --threads \${GALAXY_SLOTS:-1}
16c923816e87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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23 -o .
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24 #end if
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25 #if str($single_paired.single_paired_selector) == 'single':
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26 --single
1
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27 #set $single_reads = $single_paired.reads
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28 --fragment-length $single_paired.fragment_length
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29 --sd $single_paired.sd
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30 '$single_reads'
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31 #else:
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32 #if str($single_paired.collection.collection_selector) == 'datasets':
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7f698e0094e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit c695bedd2174ac3a0e2f4c0b1f982a9e047a5302
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33 #set $forward_reads = $single_paired.collection.forward
7f698e0094e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit c695bedd2174ac3a0e2f4c0b1f982a9e047a5302
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34 #set $reverse_reads = $single_paired.collection.reverse
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35 #else:
1
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36 #set $forward_reads = $single_paired.collection.reads.forward
7f698e0094e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit c695bedd2174ac3a0e2f4c0b1f982a9e047a5302
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37 #set $reverse_reads = $single_paired.collection.reads.reverse
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38 #end if
1
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39 #set $reads = "'%s' '%s'" % ($forward_reads, $reverse_reads)
7f698e0094e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit c695bedd2174ac3a0e2f4c0b1f982a9e047a5302
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40 $reads
0
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41 #end if
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42 #if $pseudobam:
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43 | samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -o '$pseudobam_output' -
16c923816e87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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44 #end if
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45 && cat run_info.json
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46 ]]>
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47 </command>
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48 <inputs>
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49 <conditional name="reference_genome">
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50 <param name="reference_genome_source" type="select" label="Reference genome for quantification">
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51 <option value="indexed" selected="true">Use a built-in genome</option>
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52 <option value="history">Use a genome from history</option>
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53 </param>
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54 <when value="indexed">
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55 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy administrator">
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56 <options from_data_table="kallisto_indexes">
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57 <filter type="sort_by" column="2" />
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58 <validator type="no_options" message="No genomes are available for the selected input dataset" />
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59 </options>
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60 </param>
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61 </when>
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62 <when value="history">
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63 <param name="reference" type="data" format="fasta" label="FASTA reference genome" />
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64 </when>
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65 </conditional>
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66 <conditional name="single_paired">
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67 <param name="single_paired_selector" type="select" label="Single-end or paired reads">
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68 <option value="single" selected="true">Single-end</option>
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69 <option value="paired">Paired</option>
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70 </param>
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71 <when value="single">
1
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72 <param name="reads" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
0
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73 <param name="fragment_length" argument="--fragment-length" type="integer" value="200" label="Average fragment length" help="Illumina typically produces reads of 180-200bp" />
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74 <param argument="--sd" type="integer" value="20" label="Estimated standard deviation of fragment length" />
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75 </when>
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76 <when value="paired">
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77 <conditional name="collection">
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78 <param name="collection_selector" type="select" label="Collection or individual datasets">
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79 <option value="datasets" selected="true">Individual files</option>
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80 <option value="collection">Pair or list of pairs</option>
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81 </param>
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82 <when value="datasets">
1
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83 <param name="forward" type="data" format="fastq,fastq.gz" label="Forward reads" />
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84 <param name="reverse" type="data" format="fastq,fastq.gz" label="Reverse reads" />
0
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85 </when>
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86 <when value="collection">
1
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87 <param name="reads" type="data_collection" format="fastq,fastq.gz" collection_type="paired" label="Collection of reads" />
0
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88 </when>
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89 </conditional>
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90 </when>
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91 </conditional>
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92 <param argument="--bias" type="boolean" truevalue="--bias" falsevalue="" label="Perform sequence based bias correction" />
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93 <param name="bootstrap_samples" argument="--bootstrap-samples" type="integer" value="0" label="Number of bootstrap samples" help="default: 0" />
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94 <param argument="--seed" type="integer" value="42" label="Seed for the bootstrap sampling" help="default: 42" />
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95 <param argument="--fusion" type="boolean" truevalue="--fusion" falsevalue="" label="Search for fusions" help="for Pizzly" />
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96 <param argument="--pseudobam" type="boolean" truevalue="--pseudobam" falsevalue="" label="Output pseudoalignments in BAM format" />
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97 </inputs>
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98 <outputs>
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99 <data format="h5" name="abundance_h5" from_work_dir="abundance.h5" label="${tool.name} on ${on_string}: Abundances (HDF5)" />
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100 <data format="tabular" name="abundance_tab" from_work_dir="abundance.tsv" label="${tool.name} on ${on_string}: Abundances (tabular)" />
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101 <data format="bam" name="pseudobam_output" label="${tool.name} on ${on_string}: Pseudoalignments">
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102 <filter>pseudobam</filter>
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103 </data>
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104 </outputs>
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105 <tests>
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106 <test>
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107 <param name="reference_genome_source" value="history" />
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108 <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
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109 <param name="single_paired_selector" value="paired" />
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110 <param name="collection_selector" value="datasets" />
1
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111 <param name="forward" ftype="fastq" value="mm10_chrM-1.f.fq" />
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112 <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq" />
0
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113 <output name="abundance_tab" file="kallisto_quant_out1.tab" ftype="tabular" />
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114 </test>
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115 <test>
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116 <param name="reference_genome_source" value="history" />
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117 <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
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118 <param name="single_paired_selector" value="paired" />
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119 <param name="collection_selector" value="collection" />
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120 <param name="reads">
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121 <collection type="paired">
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122 <element name="forward" value="mm10_chrM-1.f.fq" />
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123 <element name="reverse" value="mm10_chrM-1.r.fq" />
0
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124 </collection>
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125 </param>
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126 <output name="abundance_tab" file="kallisto_quant_out2.tab" ftype="tabular" />
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127 </test>
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128 <test>
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129 <param name="reference_genome_source" value="history" />
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130 <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
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131 <param name="single_paired_selector" value="single" />
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132 <param name="collection_selector" value="collection" />
1
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133 <param name="reads" ftype="fastq" value="mm10_chrM-1.f.fq" />
0
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134 <output name="abundance_tab" file="kallisto_quant_out3.tab" ftype="tabular" />
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135 </test>
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136 <test>
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137 <param name="reference_genome_source" value="history" />
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138 <param name="reference" ftype="fasta" value="felCat8_chrM.fa" />
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139 <param name="single_paired_selector" value="paired" />
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140 <param name="collection_selector" value="datasets" />
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141 <param name="pseudobam" value="true" />
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142 <param name="forward" ftype="fastq" value="felCat8_chrM_F.fq" />
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143 <param name="reverse" ftype="fastq" value="felCat8_chrM_R.fq" />
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144 <output name="abundance_tab" file="kallisto_quant_out4.tab" ftype="tabular" />
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145 <output name="pseudobam_output" file="kallisto_quant_out4.bam" ftype="bam" />
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146 </test>
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147 <test>
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148 <param name="reference_genome_source" value="cached" />
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149 <param name="single_paired_selector" value="paired" />
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150 <param name="collection_selector" value="datasets" />
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151 <param name="pseudobam" value="true" />
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152 <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_F.fq.gz" />
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153 <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq" />
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154 <output name="abundance_tab" file="kallisto_quant_out5.tab" ftype="tabular" />
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155 <output name="pseudobam_output" file="kallisto_quant_out5.bam" ftype="bam" />
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156 </test>
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157 </tests>
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158 <help>
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159 <![CDATA[
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160 kallisto 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. On benchmarks with standard RNA-Seq data, kallisto can quantify 30 million human reads in less than 3 minutes on a Mac desktop computer using only the read sequences and a transcriptome index that itself takes less than 10 minutes to build. Pseudoalignment of reads preserves the key information needed for quantification, and kallisto is therefore not only fast, but also as accurate as existing quantification tools. In fact, because the pseudoalignment procedure is robust to errors in the reads, in many benchmarks kallisto significantly outperforms existing tools.
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161 ]]>
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162 </help>
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163 <expand macro="citations" />
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164 </tool>