annotate macros.xml @ 18:ebab418107f5 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664
author bgruening
date Wed, 07 Dec 2022 19:31:41 +0000
parents c8903f357804
children 15cd64d7c58b
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1 <macros>
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2 <token name="@TOOL_VERSION@">1.9.0</token>
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3 <token name="@VERSION_SUFFIX@">2</token>
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4 <token name="@IDX_VERSION@">q7</token>
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5 <token name="@PROFILE_VERSION@">20.01</token>
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6 <xml name="requirements">
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">salmon</requirement>
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9 <requirement type="package" version="1.3">seqtk</requirement>
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10 <requirement type="package" version="1.16.1">samtools</requirement>
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11 <requirement type="package" version="0.2.0">vpolo</requirement>
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12 <requirement type="package" version="1.5.2">pandas</requirement>
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13 <requirement type="package" version="3.0.0">graphviz</requirement>
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14 <requirement type="package" version="1.9.3">scipy</requirement>
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15 </requirements>
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16 </xml>
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17 <xml name="orient">
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18 <param name="orientation" type="select" label="Relative orientation of reads within a pair">
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19 <option value="M">Mates are oriented in the same direction (M = matching)</option>
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20 <option value="O">Mates are oriented away from each other (O = outward)</option>
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21 <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option>
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22 </param>
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23 </xml>
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24 <xml name="stranded">
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25 <conditional name="libtype" >
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26 <param name="strandedness" type="select" label="Specify the strandedness of the reads" help="--libtype">
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27 <option value="A" selected="true">Infer automatically (A)</option>
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28 <option value="U">Not stranded (U)</option>
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29 <option value="SF">read comes from the forward strand (SF)</option>
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30 <option value="SR">read comes from the reverse strand (SR)</option>
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31 </param>
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32 <yield/>
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33 </conditional>
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34 </xml>
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35 <xml name="stranded_se">
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36 <expand macro="stranded">
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37 <when value="A"/>
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38 <when value="U"/>
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39 <when value="SF"/>
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40 <when value="SR"/>
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41 </expand>
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42 </xml>
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43 <xml name="stranded_pe">
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44 <expand macro="stranded">
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45 <when value="A">
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46 </when>
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47 <when value="U">
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48 <expand macro="orient"/>
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49 </when>
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50 <when value="SF">
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51 <expand macro="orient"/>
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52 </when>
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53 <when value="SR">
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54 <expand macro="orient"/>
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55 </when>
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56 </expand>
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57 </xml>
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58 <xml name="index">
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59 <conditional name="refTranscriptSource">
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60 <param name="TranscriptSource" type="select" label="Select a reference transcriptome from your history or use a built-in index?"
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61 help="Built-ins were indexed using default options">
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62 <option value="indexed">Use a built-in index</option>
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63 <option value="history" selected="True">Use one from the history</option>
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64 </param>
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65 <when value="indexed">
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66 <param name="index" type="select" label="Select a reference transcriptome" help="If your transcriptome of interest is not listed, contact your Galaxy admin">
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67 <options from_data_table="salmon_indexes_versioned">
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68 <filter type="sort_by" column="2"/>
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69 <filter type="static_value" column="4" value="@IDX_VERSION@" />
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70 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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71 </options>
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72 </param>
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73 </when> <!-- build-in -->
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74 <when value="history">
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75 <section name="s_index" title="Salmon index" expanded="true">
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76 <param name="fasta" type="data" format="fasta" label="Transcripts FASTA file"/>
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77 <param name="genome" type="data" format="fasta" optional="true" label="Reference genome"
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78 help="The reference genome is required for generating a decoy-away index. The decoy sequences are regions of the target genome
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79 that are sequence similar to annotated transcripts. These are the regions of the genome most likely to cause mismapping." />
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80 <param name="kmer" type="integer" value="31" label="Kmer length"/>
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81 <param name="phash" type="boolean" label="Perfect Hash" truevalue="--perfectHash" falsevalue="" checked="false"
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82 help="Build the index using a perfect hash rather than a dense hash. This will require less memory (especially during quantification),
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83 but will take longer to construct"/>
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84 </section>
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85 </when>
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86 </conditional>
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87 </xml>
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88 <xml name="reads">
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89 <section name="input" title="Data input" expanded="True">
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90 <conditional name="single_or_paired">
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91 <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?">
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92 <option value="single">Single-end</option>
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93 <option value="paired">Paired-end</option>
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94 <option value="paired_collection">Paired-end Dataset Collection</option>
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95 <option value="paired_interleaved">Paired-end data from single interleaved dataset</option>
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96 </param>
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97 <when value="single">
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98 <param name="input_singles" type="data" format="fastq,fasta,fastq.gz,fastq.bz2" label="FASTQ/FASTA file" help="FASTQ file." />
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99 <expand macro="stranded_se"/>
10
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100 </when>
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101 <when value="paired">
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102 <param name="input_mate1" type="data" format="fastq,fasta,fastq.gz,fastq.bz2,fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Mate pair 1" help="FASTQ file." />
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103 <param name="input_mate2" type="data" format="fastq,fasta,fastq.gz,fastq.bz2,fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Mate pair 2" help="FASTQ file." />
16
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104 <expand macro="stranded_pe"/>
10
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105 </when>
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106 <when value="paired_collection">
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107 <param name="input_1" format="fastq,fasta,fastq.gz,fastq.bz2,fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
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108 <expand macro="stranded_pe"/>
10
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109 </when>
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110 <when value="paired_interleaved">
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111 <param name="input_1" format="fastq,fasta,fastq.gz,fastq.bz2,fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="Interleaved FASTQ file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;. --interleaved"/>
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112 <expand macro="stranded_pe"/>
10
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113 </when>
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114 </conditional>
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115 </section>
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116 <param argument="--type" type="select" label="Type of index" help="When using quasi, orphaned reads will be considered when performing lightweight-alignment.">
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117 <option value="quasi" selected="True">quasi</option>
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118 </param>
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119 <!--Salmon quant type select: reads-based or alignment-based-->
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120 <param name="discardOrphansQuasi" type="boolean" truevalue="--discardOrphansQuasi" falsevalue="" checked="False"
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121 label="Discard orphan quasi"
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122 help="Discard orphan mappings in quasi-mapping mode. If this flag is passed then only paired mappings will be considered toward quantification estimates. The default behavior is to consider orphan mappings if no valid paired mappings exist."/>
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123 <conditional name="validmap">
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124 <param name="validateMappings" type="boolean" truevalue="--validateMappings" falsevalue="" checked="False"
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125 label="Validate mappings"
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126 help="Validate mappings using alignment-based verifcation. If this flag is passed, quasi-mappings will be validated to ensure that they could give rise to a reasonable alignment before they are further used for quantification."/>
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127 <when value="--validateMappings">
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128 <param name="minScoreFraction" type="float" value="0.65" min="0.0" max="0.99"
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129 label="Min Score Fraction"
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130 help="The fraction of the optimal possible alignment score that a mapping must achieve in order to be considered valid. Should be in (0,1]."/>
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131 <param name="maxMMPExtension" type="integer" optional="True"
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132 label="Sets the maximum allowable MMP extension when collecting suffix array intervals to be used in chaining. This prevents MMPs from becoming too long, and potentially masking intervals that would uncover other good quasi-mappings for the read. This heuristic mimics the idea of the maximum mappable safe prefix (MMSP) in selective alignment. Setting a smaller value will potentially allow for more sensitive, but slower, mapping."/>
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133 <param name="matchScore" argument="--ma" type="integer" value="2"
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134 label="Match Score"
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135 help="The value given to a match between read and reference nucleotides in an alignment."/>
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136 <param name="mismatchPenalty" argument="--mp" type="integer" value="4"
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137 label="Mismatch Penalty"
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138 help="The value given to a mis-match between read and reference nucleotides in an alignment. This will be cast to a negative value."/>
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139 <param name="gapOpenPenalty" argument="--go" type="integer" value="5"
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140 label="Gap Open Penalty"
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141 help="The value given to a gap opening in an alignment."/>
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142 <param name="gapExtensionPenalty" argument="--ge" type="integer" value="3"
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143 label="Gap Extension Penalty"
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144 help="The value given to a gap extension in an alignment."/>
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145 <param name="mimicBT2" type="boolean" truevalue="--mimicBT2" falsevalue="" checked="False"
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146 label="Mimic Bowtie 2"
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147 help=" Set flags to mimic parameters similar to Bowtie2 with --no-discordant and --no-mixed flags. This increases disallows dovetailing reads, and discards orphans. Note, this does not impose the very strict parameters assumed by RSEM+Bowtie2, like gapless alignments. For that behavior, use the --mimiStrictBT2 flag "/>
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148 <param name="mimicStrictBT2" type="boolean" truevalue="--mimicStrictBT2" falsevalue="" checked="False"
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149 label="Mimic Strict Bowtie 2"
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150 help="Set flags to mimic the very strict parameters used by RSEM+Bowtie2. This increases --minScoreFraction to 0.8, disallows dovetailing reads, discards orphans, and disallows gaps in alignments."/>
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151 <param name="hardFilter" type="boolean" truevalue="--hardFilter" falsevalue="" checked="False"
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152 label="Hard Filter"
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153 help="Instead of weighting mappings by their alignment score, this flag will discard any mappings with sub-optimal alignment score. The default option of soft-filtering (i.e. weighting mappings by their alignment score) usually yields slightly more accurate abundance estimates but this flag may be desirable if you want more accurate 'naive' equivalence classes, rather than range factorized equivalence classes."/>
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154 </when>
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155 <when value=""/>
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156 </conditional>
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157 <param name="consensusSlack" type="integer" optional="True" value="0"
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158 label="Consensus Slack"
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159 help="The amount of slack allowed in the quasi-mapping consensus mechanism. Normally, a transcript must cover all hits to be considered for mapping. If this is set to a value, X, greater than 0, then a transcript can fail to cover up to X hits before it is discounted as a mapping candidate. The default value of this option is 1 if --validateMappings is given and 0 otherwise."/>
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160 <param name="dovetail" label="Allow Dovetail" type="boolean" truevalue="--allowDovetail" falsevalue="" checked="False" help="Allow dovetail mappings"/>
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161 <param name="recoverOrphans" label="Recover Orphans" type="boolean" truevalue="--recoverOrphans" falsevalue="" checked="False"
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162 help="Attempt to recover the mates of orphaned reads. This uses edlib for orphan recovery, and so introduces some computational overhead, but it can improve sensitivity."/>
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163 <conditional name="bam_options">
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164 <param argument="--writeMappings" type="select" label="Write Mappings to BAM File" help="If this option is provided, then the quasi-mapping results will be written out in SAM-compatible format. By default, output will be directed to stdout, but an alternative file name can be provided instead">
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165 <option value="--writeMappings=./output/samout.sam">Enabled</option>
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166 <option value="" selected="true">Disabled</option>
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167 </param>
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168 <when value="--writeMappings=./output/samout.sam">
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169 <param argument="--writeQualities" type="boolean" truevalue="--writeQualities" falsevalue="" checked="false" label="Write qualities" help="If this flag is
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170 provided, then the output SAM file will contain quality strings as well as read sequences." />
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171 </when>
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172 <when value=""/>
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173 </conditional>
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174 <param name="consistentHits" type="boolean" truevalue="--consistentHits" falsevalue="" checked="False"
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175 label="Consistent Hits"
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176 help="Force hits gathered during quasi-mapping to be 'consistent' (i.e. co-linear and approximately the right distance apart)."/>
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177 <param name="quasiCoverage" type="integer" optional="True" label="Quasi Coverage"
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178 help="[Experimental]: The fraction of the read that must be covered by MMPs (of length >= 31) if this read is to be considered as 'mapped'. This may help to avoid 'spurious' mappings. A value of 0 (the default) denotes no coverage threshold (a single 31-mer can yield a mapping). Since coverage by exact matching, large, MMPs is a rather strict condition, this value should likely be set to something low, if used."/>
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179 </xml>
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180 <xml name="align">
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181 <param name="afile" type="data" format="qname_input_sorted.bam,qname_sorted.bam" label="Alignment file"/>
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182 <param argument="--ont" type="boolean" truevalue="--ont" falsevalue="" label="Is this Alignment file a Oxford Nanopore Technologies (ONT) dataset ?" help="Select this for both cDNA and direct RNA ONT datasets. Enables an alignment error model designed to work with long-read alignments and disables the length effect in the generative model when computing the conditional probability of observing a fragment given that it arises from a specific transcript. This is because in long-read sequencing, we do not expect to observe (i.e. sequence) multiple fragments from the same molecule, and thus we do not expect the transcript length to directly affect the observed fragment count directly"/>
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183 <param name="transcript" type="data" format="fasta,fa" label="Transcript file"/>
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184 <expand macro="stranded_se"/>
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185 <param name="discardOrphans" type="boolean" truevalue="--discardOrphans" falsevalue="" checked="False"
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186 label="Discard orphans"
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187 help="Discard orphan alignments in the input. If this flag is passed, then only paired alignments will be considered toward quantification estimates. The default behavior is to consider orphan alignments if no valid paired mappings exist."/>
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188 <param name="noErrorModel" type="boolean" truevalue="--noErrorModel" falsevalue="" checked="False"
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189 label="No Error Model"
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190 help="Turn off the alignment error model, which takes into account the the observed frequency of different types of mismatches / indels when computing the likelihood of a given alignment. Turning this off can speed up alignment-based salmon, but can harm quantification accuracy."/>
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191 <param name="numErrorBins" type="integer" optional="True" value="6"
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192 label="Number of Error Bins"
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193 help="The number of bins into which to divideeach read when learning and applying the error model. For example, a value of 10 would mean that effectively, a separate error model is learned and applied to each 10th of the read, whilea value of 3 would mean that a separate error model is applied to the read beginning (first third), middle (second third) and end (final third)."/>
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194 <param name="sampleOut" type="boolean" truevalue="--sampleOut" falsevalue="" checked="False"
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195 label="Sample out"
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196 help="Write a 'postSample.bam' file in the output directory that will sample the input alignments according to the estimated transcript abundances. If you're going to perform downstream analysis of the alignments with tools which don't, themselves, take fragment assignment ambiguity into account, you should use this output"/>
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197 <param name="sampleUnaligned" type="boolean" truevalue="--sampleUnaligned" falsevalue="" checked="False"
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198 label="Sample unaligned"
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199 help="In addition to sampling the aligned reads, also write the un-aligned reads to 'postSample.bam'."/>
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200 <param name="gencode" type="boolean" truevalue="--gencode" falsevalue="" checked="False"
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201 label="Gencode"
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202 help="This flag will expect the input transcript fasta to be in GENCODE format, and will split the transcript name at the first '|' character. These reduced names will be used in the output and when looking for these transcripts in a gene to transcript GTF."/>
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203 </xml>
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204 <xml name="quantboth">
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205 <param name="geneMap" type="data" format="tabular,gff,gtf" optional="True"
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206 label="File containing a mapping of transcripts to genes"
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207 help="If this file is provided Salmon will output both quant.sf and quant.genes.sf files, where the latter contains aggregated gene-level abundance estimates. The transcript to gene mapping should be provided as either a GTF file, or a in a simple tab-delimited format where each line contains the name of a transcript and the gene to which it belongs separated by a tab."/>
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208 <param name="seqBias" type="boolean" truevalue="--seqBias" falsevalue="" checked="False"
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209 label="Perform sequence-specific bias correction"/>
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210 <param name="gcBias" type="boolean" truevalue="--gcBias" falsevalue="" checked="False"
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211 label="Perform fragment GC bias correction"/>
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212 <param name="incompatPrior" type="float" optional="True" min="0.0" max="1" value="0"
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213 help="Sets the prior probability that an alignment that disagrees with the specified library type (orientation and strandedness) results from the true fragment origin. Setting this to 0 specifies that alignments that disagree with the library type should be 'impossible', while setting it to 1 says that alignments that disagree with the library type are no less likely than those that do"/>
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214 <param name="meta" type="boolean" truevalue="--meta" falsevalue="" checked="False"
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215 label="Meta"
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216 help="If you're using Salmon on a metagenomic dataset, consider setting this flag to disable parts of the abundance estimation model that make less sense for metagenomic data."/>
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217 <!--Salmon quant advanced options: available to both kinds of quant-->
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218 <section name="adv" title="Additional Options">
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219 <param name="skipQuant" type="boolean" truevalue="--skipQuant" falsevalue="" checked="False"
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220 label="skipQuant" help="Skip performing the actual transcript quantification (including any Gibbs sampling or bootstrapping)."/>
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221 <param name="dumpEq" type="boolean" truevalue="--dumpEq" falsevalue="" checked="False"
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222 label="Dump equivalence class counts"
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223 help="Dump the equivalence class counts that were computed during quasi-mapping."/>
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224 <param name="dumpEqWeights" type="boolean" truevalue="--dumpEqWeights" falsevalue="" checked="False"
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225 label="Dump equivalence class counts including rich weights"
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226 help="Includes 'rich' equivlance class weights in the output when equivalence class information is being dumped to file."/>
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227 <param name="minAssignedFrags" type="integer" optional="True" label="Minimum assigned fragments"
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228 help="The minimum number of fragments that must be assigned to the transcriptome for quantification to proceed."/>
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229 <param name="biasSpeedSamp" type="integer" value="5" optional="True"
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230 label="The value at which the fragment length PMF is down-sampled when evaluating GC fragment bias." help="Larger values speed up effective length correction, but may decrease the fidelity of bias modeling results."/>
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231 <param name="fldMax" type="integer" value="1000" optional="True"
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232 label="The maximum fragment length to consider when building the empirical distribution."/>
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233 <param name="fldMean" type="integer" value="250" optional="True"
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234 label="The mean used in the fragment length distribution prior"
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235 help="If single end reads are being used for quantification, or there are an insufficient number of uniquely mapping reads when performing paired-end quantification to estimate the empirical fragment length distribution, then use this value to calculate effective lengths."/>
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236 <param name="fldSD" type="integer" value="25" optional="True"
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237 label="Standard deviation"
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238 help="The standard deviation used in the fragment length distribution prior."/>
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239 <param name="forgettingFactor" type="float" value="0.65000000000000002" optional="True"
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240 label="The forgetting factor used in the online learning schedule."
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241 help=" A smaller value results in quicker learning, but higher variance and may be unstable. A larger value results in slower learning but may be more stable. Value should be in the interval (0.5, 1.0]." />
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242 <param name="initUniform" type="boolean" truevalue="--initUniform" falsevalue="" checked="False"
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243 label="Initialization with uniform parameters"
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244 help="initialize the offline inference with uniform parameters, rather than seeding with online parameters." />
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245 <param name="maxReadOcc" type="integer" value="100" optional="True"
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246 label="Maximal read mapping occurence"
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247 help="Reads mapping to more than this many places won't be considered."/>
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248 <param name="noLengthCorrection" type="boolean" truevalue="--noLengthCorrection" falsevalue=""
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249 label="No length correction"
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250 help="[experimental] : Entirely disables length correction when estimating the abundance of transcripts. This option can be used with protocols where one expects that fragments derive from their underlying targets without regard to that target's length (e.g. QuantSeq)"/>
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251 <param name="noEffectiveLengthCorrection" type="boolean" truevalue="--noEffectiveLengthCorrection" falsevalue="" checked="False"
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252 label="Disable effective length correction"
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253 help="Disables effective length correction when computing the probability that a fragment was generated from a transcript. If this flag is passed in, the fragment length distribution is not taken into account when computing this probability."/>
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254 <param name="noFragLengthDist" type="boolean" truevalue="--noFragLengthDist" falsevalue="" checked="False"
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255 label="Ignore fragment length distribution"
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256 help="[experimental] : Don't consider concordance with the learned fragment length distribution when trying to determine the probability that a fragment has originated from a specified location. Normally, Fragments with unlikely lengths will be assigned a smaller relative probability than those with more likely lengths. When this flag is passed in, the observed fragment length has no effect on that fragment's a priori probability." />
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257 <param name="noBiasLengthThreshold" type="boolean" truevalue="--noBiasLengthThreshold" falsevalue="" checked="False"
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258 label="[experimental] : If this option is enabled, then no (lower) threshold will be set on how short bias correction can make effecctive lengths."
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259 help="This can increase the precision of bias correction, but harm robustness. The default correction applies a threshold." />
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260 <param name="numBiasSamples" type="integer" value="2000000" optional="True"
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261 label="Number of fragment mappings to use when learning the sequence-specific bias model."/>
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262 <param name="numAuxModelSamples" type="integer" value="5000000" optional="True"
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263 label="The first numAuxModelSamples are used to train the auxiliary model parameters."
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264 help="(e.g. fragment length distribution, bias, etc.). After ther first numAuxModelSamples observations the auxiliary model parameters will be assumed to have converged and will be fixed." />
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265 <param name="numPreAuxModelSamples" type="integer" value="5000" optional="True"
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266 label="The first numPreAuxModelSamples will have their assignment likelihoods and contributions to the transcript abundances computed without applying any auxiliary models."
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267 help=" The purpose of ignoring the auxiliary models for the first numPreAuxModelSamples observations is to avoid applying these models before thier parameters have been learned sufficiently well." />
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268 <param name="useEM" type="boolean" truevalue="--useEM" falsevalue="" checked="False"
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269 label="Use the traditional EM algorithm for optimization in the batch passes."
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270 help=""/>
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271 <param name="rangeFactorizationBins" type="integer" value="0" label="Range of factorization bins"
16
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272 help="Factorizes the likelihood used in quantification by adopting a new notion of equivalence classes based on the conditional probabilities with which fragments are generated from different transcripts. This is a more fine-grained factorization than the normal rich equivalence classes. The default value (0) corresponds to the standard rich equivalence classes, and larger values imply a more fine-grained factorization. If range factorization is enabled, a common value to select for this parameter is 4."/>
10
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273 <param name="numGibbsSamples" type="integer" value="0" optional="True"
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274 label="Number of Gibbs sampling rounds to perform."
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275 help="" />
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276 <param name="noGammaDraw" type="boolean" truevalue="--noGammaDraw" falsevalue="" checked="False"
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277 label="No gamma draw"
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278 help="This switch will disable drawing transcript fractions from a Gamma distribution during Gibbs sampling. In this case the sampler does not account for shot-noise, but only assignment ambiguity"/>
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279 <param name="numBootstraps" type="integer" value="0" optional="True"
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280 label="Number of bootstrap samples to generate. Note: This is mutually exclusive with Gibbs sampling."
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281 help="" />
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282 <param name="bootstrapReproject" type="boolean" truevalue="--bootstrapReproject" falsevalue="" checked="False"
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283 label="Bootstrap reproject"
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284 help="This switch will learn the parameter distribution from the bootstrapped counts for each sample, but will reproject those parameters onto the original equivalence class counts."/>
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285 <param name="thinningFactor" type="integer" value="16" optional="true" label="Thinning factor"
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286 help="Number of steps to discard for every sample kept from the Gibbs chain. The larger this number, the less chance that subsequent samples are auto-correlated, but the slower sampling becomes."/>
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287 <param name="perTranscriptPrior" type="boolean" truevalue="--perTranscriptPrior" falsevalue="" checked="False"
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288 label="The prior will be interpreted as a transcript-level prior."
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289 help="either the default or the argument provided via --vbPrior" />
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290 <param name="sigDigits" type="integer" value="3"
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291 label="Significant Digits"
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292 help="The number of significant digits to write when outputting the EffectiveLength and NumReads columns."/>
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293 <param name="vbPrior" type="float" value="1.0000000000000001e-05" optional="True"
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294 label="The prior that will be used in the VBEM algorithm."
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295 help="This is interpreted as a per-nucleotide prior, unless the --perTranscriptPrior flag is also given, in which case this is used as a transcript-level prior." />
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296 <param name="writeOrphanLinks" type="boolean" truevalue="--writeOrphanLinks" falsevalue="" checked="False" label="Write orphan links"
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297 help="Write the transcripts that are linked by orphaned reads."/>
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298 <param name="writeUnmappedNames" type="boolean" truevalue="--writeUnmappedNames" falsevalue="" checked="False"
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299 label="Write the names of un-mapped reads to the file unmapped_names.txt."
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300 help=""/>
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301 </section>
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302 </xml>
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303 <xml name="quantmerge">
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304 <repeat name="quantfiles" title="Quant file and names">
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305 <param name="quants" type="data" format="tsv,tabular"
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306 label="Salmon quant tabular output files"/>
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307 <param name="names" type="text" label="One-word sample names" optional="True"/>
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308 </repeat>
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309 <param name="column" type="select" label="Columns"
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310 help="Name of columns that will be merged in the output file">
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311 <option value="len" selected="True">Length</option>
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312 <option value="elen">Effective Length</option>
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313 <option value="tpm">Transcripts per Million</option>
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314 <option value="numreads">NumReads</option>
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315 </param>
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316 <param name="genes" type="boolean" truevalue="--genes" falsevalue="" checked="False"
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317 label="Genes" help="Use gene quantifications instead of transcript"/>
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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318 <param name="missing" type="integer" label="Missing" optional="True" help="The value of missing values"/>
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
319 </xml>
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
320 <xml name="citations">
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
321 <citations>
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
322 <citation type="doi">10.1186/s13059-019-1670-y</citation>
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
323 <citation type="doi">10.1038/nmeth.4197</citation>
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
324 </citations>
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
325 </xml>
13
e3d32471da11 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 30fe16f7d786e4b0c43b8333853fc56c59f6c664"
bgruening
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diff changeset
326 <token name="@bam_sort@"><![CDATA[samtools sort -@ \${GALAXY_SLOTS} --output-fmt=BAM -o ./output/bamout.bam]]></token>
10
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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327 <token name="@indexing@"><![CDATA[
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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diff changeset
328 mkdir ./index &&
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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329 mkdir ./output &&
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
330 #if $quant_type.refTranscriptSource.TranscriptSource != "indexed":
17
c8903f357804 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
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diff changeset
331 #if $quant_type.refTranscriptSource.s_index.genome
c8903f357804 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
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diff changeset
332 cat '${quant_type.refTranscriptSource.s_index.genome}' | grep "^>" | cut -d " " -f 1 > 'decoys.txt' &&
c8903f357804 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
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diff changeset
333 sed -i.bak -e 's/>//g' 'decoys.txt' &&
c8903f357804 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
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diff changeset
334 cat '${quant_type.refTranscriptSource.s_index.fasta}' '${quant_type.refTranscriptSource.s_index.genome}' > 'input_index.fasta' &&
c8903f357804 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 16
diff changeset
335 #else
c8903f357804 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
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diff changeset
336 ln -s '${quant_type.refTranscriptSource.s_index.fasta}' 'input_index.fasta' &&
c8903f357804 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
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337 #end if
10
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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338 salmon index -i ./index
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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339 --kmerLen '${quant_type.refTranscriptSource.s_index.kmer}'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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340 --gencode
17
c8903f357804 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
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341 --threads "\${GALAXY_SLOTS:-4}"
c8903f357804 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
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342 --transcripts 'input_index.fasta'
c8903f357804 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
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diff changeset
343 #if $quant_type.refTranscriptSource.s_index.genome
c8903f357804 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
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diff changeset
344 --decoy 'decoys.txt'
c8903f357804 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
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345 #end if
10
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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346 &&
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
347 #set $index_path = './index'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
348 #else
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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349 #set $index_path = $quant_type.refTranscriptSource.index.fields.path
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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350 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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351 ]]>
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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352 </token>
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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353 <token name="@salreads@"><![CDATA[
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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354 #set compressed = 'no'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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355 #if $quant_type.input.single_or_paired.single_or_paired_opts == 'single':
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
356 #if $quant_type.input.single_or_paired.input_singles.ext == 'fasta':
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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357 #set $ext = 'fasta'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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358 #else:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
359 #if $quant_type.input.single_or_paired.input_singles.is_of_type("fastq.gz", "fastqsanger.gz"):
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
360 #set compressed = 'GZ'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
361 #else if $quant_type.input.single_or_paired.input_singles.is_of_type("fastq.bz2", "fastqsanger.bz2"):
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
362 #set compressed = 'BZ2'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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363 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
364 #set $ext = 'fastq'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
365 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
366 ln -s $quant_type.input.single_or_paired.input_singles ./single.$ext &&
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
367 #else if $quant_type.input.single_or_paired.single_or_paired_opts == 'paired':
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
368 #if $quant_type.input.single_or_paired.input_mate1.ext == 'fasta':
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
369 #set $ext = 'fasta'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
370 #else:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
371 #if $quant_type.input.single_or_paired.input_mate1.is_of_type("fastq.gz", "fastqsanger.gz"):
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
372 #set compressed = 'GZ'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
373 #else if $quant_type.input.single_or_paired.input_mate1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
374 #set compressed = 'BZ2'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
375 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
376 #set $ext = 'fastq'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
377 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
378 ln -s $quant_type.input.single_or_paired.input_mate1 ./mate1.$ext &&
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
379 ln -s $quant_type.input.single_or_paired.input_mate2 ./mate2.$ext &&
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
380 #else if $quant_type.input.single_or_paired.single_or_paired_opts == 'paired_collection':
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
381 #if $quant_type.input.single_or_paired.input_1.forward.ext == 'fasta':
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
382 #set $ext = 'fasta'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
383 #else:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
384 #if $quant_type.input.single_or_paired.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
385 #set compressed = 'GZ'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
386 #else if $quant_type.input.single_or_paired.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
387 #set compressed = 'BZ2'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
388 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
389 #set $ext = 'fastq'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
390 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
391 ln -s '${quant_type.input.single_or_paired.input_1.forward}' ./mate1.$ext &&
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
392 ln -s '${quant_type.input.single_or_paired.input_1.reverse}' ./mate2.$ext &&
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
393 #else if '$quant_type.input.single_or_paired.single_or_paired_opts' == 'paired_interleaved':
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
394 #if $quant_type.input.single_or_paired.input_1.ext == 'fasta':
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
395 #set $ext = 'fasta'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
396 #else:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
397 #if $quant_type.input.single_or_paired.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
398 #set compressed = 'GZ'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
399 #else if $quant_type.input.single_or_paired.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
400 #set compressed = 'BZ2'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
401 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
402 #set $ext = 'fastq'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
403 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
404 ln -s '$quant_type.input.single_or_paired.input_1' ./mate1.$ext &&
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
405 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
406 #if $geneMap:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
407 ln -s '$geneMap' ./geneMap.${geneMap.ext} &&
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
408 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
409
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
410 salmon quant
14
b265be7af3db "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents: 13
diff changeset
411 --index '$index_path'
10
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
412 #if $quant_type.input.single_or_paired.single_or_paired_opts == 'single':
16
49121db48873 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 14
diff changeset
413 --libType ${quant_type.input.single_or_paired.libtype.strandedness}
10
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
414 #if $compressed == 'GZ':
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
415 --unmatedReads <(zcat < ./single.$ext)
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
416 #else if $compressed == 'BZ2':
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
417 --unmatedReads <(bzcat < ./single.$ext)
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
418 #else:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
419 --unmatedReads ./single.$ext
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
420 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
421 #else:
16
49121db48873 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 14
diff changeset
422 --libType
49121db48873 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 14
diff changeset
423 #if $quant_type.input.single_or_paired.libtype.strandedness == 'A'
49121db48873 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 14
diff changeset
424 A
49121db48873 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 14
diff changeset
425 #else
49121db48873 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 14
diff changeset
426 ${quant_type.input.single_or_paired.libtype.orientation}${quant_type.input.single_or_paired.libtype.strandedness}
49121db48873 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 14
diff changeset
427 #end if
10
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
428 #if $quant_type.input.single_or_paired.single_or_paired_opts == 'paired_interleaved':
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
429 #if $compressed == 'BZ2':
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
430 --mates1 <(bzcat < ./mate1.$ext | seqtk seq -1)
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
431 --mates2 <(bzcat < ./mate1.$ext | seqtk seq -2)
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
432 #else:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
433 --mates1 <(seqtk seq -1 ./mate1.$ext)
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
434 --mates2 <(seqtk seq -2 ./mate1.$ext)
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
435 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
436 #else:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
437 #if $compressed == 'GZ':
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
438 --mates1 <(zcat < ./mate1.$ext)
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
439 --mates2 <(zcat < ./mate2.$ext)
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
440 #else if $compressed == 'BZ2':
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
441 --mates1 <(bzcat < ./mate1.$ext)
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
442 --mates2 <(bzcat < ./mate2.$ext)
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
443 #else:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
444 --mates1 ./mate1.$ext
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
445 --mates2 ./mate2.$ext
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
446 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
447 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
448 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
449 --threads "\${GALAXY_SLOTS:-4}"
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
450 ${quant_type.discardOrphansQuasi}
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
451 ${quant_type.validmap.validateMappings}
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
452 #if $quant_type.validmap.validateMappings:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
453 #if $quant_type.validmap.minScoreFraction:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
454 --minScoreFraction '${quant_type.validmap.minScoreFraction}'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
455 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
456 #if $quant_type.validmap.maxMMPExtension:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
457 --maxMMPExtension '${quant_type.validmap.maxMMPExtension}'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
458 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
459 #if $quant_type.validmap.matchScore:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
460 --ma '${$quant_type.validmap.matchScore}'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
461 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
462 #if $quant_type.validmap.mismatchPenalty:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
463 --mp '${$quant_type.validmap.mismatchPenalty}'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
464 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
465 #if $quant_type.validmap.gapOpenPenalty:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
466 --go '${$quant_type.validmap.gapOpenPenalty}'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
467 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
468 #if $quant_type.validmap.gapExtensionPenalty:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
469 --ge '${$quant_type.validmap.gapExtensionPenalty}'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
470 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
471 ${$quant_type.validmap.mimicBT2}
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
472 ${$quant_type.validmap.mimicStrictBT2}
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
473 ${$quant_type.validmap.hardFilter}
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
474 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
475 #if $quant_type.consensusSlack:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
476 --consensusSlack '${quant_type.consensusSlack}'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
477 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
478 ${quant_type.dovetail}
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
479 ${quant_type.recoverOrphans}
17
c8903f357804 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 16
diff changeset
480 ${quant_type.bam_options.writeMappings}
c8903f357804 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 16
diff changeset
481 #if $quant_type.bam_options.writeMappings:
c8903f357804 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 16
diff changeset
482 ${quant_type.bam_options.writeQualities}
c8903f357804 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 16
diff changeset
483 #end if
10
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
484 ${quant_type.consistentHits}
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
485 #if $quant_type.quasiCoverage:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
486 --quasiCoverage '${quant_type.quasiCoverage}'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
487 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
488 ]]>
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
489 </token>
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
490 <token name="@salalign@"><![CDATA[
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
491 #if $geneMap:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
492 ln -s "$geneMap" ./geneMap.${geneMap.ext} &&
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
493 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
494 salmon quant
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
495 -t '${quant_type.transcript}'
16
49121db48873 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 14
diff changeset
496 -l '${quant_type.libtype.strandedness}'
10
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
497 -a '${quant_type.afile}'
16
49121db48873 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 14
diff changeset
498 $quant_type.ont
10
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
499 --threads "\${GALAXY_SLOTS:-4}"
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
500 ${quant_type.discardOrphans}
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
501 ${quant_type.noErrorModel}
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
502 #if $quant_type.numErrorBins:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
503 --numErrorBins '${quant_type.numErrorBins}'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
504 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
505 ${quant_type.sampleOut}
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
506 ${quant_type.sampleUnaligned}
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
507 ${quant_type.gencode}
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
508 ]]>
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
509 </token>
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
510 <token name="@salquant@"><![CDATA[
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
511 #if $geneMap:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
512 --geneMap ./geneMap.${geneMap.ext}
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
513 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
514
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
515 ##Further basic options##
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
516
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
517 ${seqBias}
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
518 ${gcBias}
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
519 --incompatPrior '${incompatPrior}'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
520 ${meta}
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
521
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
522 ##Advanced options##
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
523
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
524 ${adv.skipQuant}
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
525 ${adv.dumpEq}
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
526 ${adv.dumpEqWeights}
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
527 #if $adv.minAssignedFrags:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
528 --minAssignedFrags '${adv.minAssignedFrags}'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
529 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
530 #if $adv.biasSpeedSamp:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
531 --biasSpeedSamp '${adv.biasSpeedSamp}'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
532 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
533 #if $adv.fldMax:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
534 --fldMax '${adv.fldMax}'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
535 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
536 #if $adv.fldMean:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
537 --fldMean '${adv.fldMean}'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
538 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
539 #if $adv.fldSD:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
540 --fldSD '${adv.fldSD}'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
541 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
542 #if $adv.forgettingFactor:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
543 --forgettingFactor '${adv.forgettingFactor}'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
544 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
545 ${adv.initUniform}
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
546 #if str($adv.maxReadOcc):
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
547 --maxReadOcc '${adv.maxReadOcc}'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
548 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
549 ${adv.noLengthCorrection}
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
550 ${adv.noEffectiveLengthCorrection}
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
551 ${adv.noFragLengthDist}
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
552 ${adv.noBiasLengthThreshold}
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
553 #if str($adv.numBiasSamples):
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
554 --numBiasSamples '${adv.numBiasSamples}'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
555 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
556 #if str($adv.numAuxModelSamples):
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
557 --numAuxModelSamples '${adv.numAuxModelSamples}'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
558 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
559 #if str($adv.numPreAuxModelSamples):
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
560 --numPreAuxModelSamples '${adv.numPreAuxModelSamples}'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
561 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
562 ${adv.useEM}
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
563 #if $adv.rangeFactorizationBins:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
564 --rangeFactorizationBins '${adv.rangeFactorizationBins}'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
565 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
566 #if str($adv.numGibbsSamples):
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
567 --numGibbsSamples '${adv.numGibbsSamples}'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
568 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
569 ${adv.noGammaDraw}
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
570 #if str($adv.numBootstraps):
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
571 --numBootstraps '${adv.numBootstraps}'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
572 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
573 ${adv.bootstrapReproject}
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
574 #if $adv.thinningFactor:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
575 --thinningFactor '${adv.thinningFactor}'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
576 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
577 ${adv.perTranscriptPrior}
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
578 --sigDigits '${adv.sigDigits}'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
579 #if $adv.vbPrior:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
580 --vbPrior '${adv.vbPrior}'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
581 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
582 ${adv.writeOrphanLinks}
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
583 ${adv.writeUnmappedNames}
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
584 -o ./output
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
585 ]]>
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
586 </token>
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
587 <token name="@qmerge@"><![CDATA[
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
588 #import re
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
589
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
590 #for $counter, $input_data in enumerate($quantfiles):
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
591 rank_of_series=$counter
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
592 mkdir ${counter}.quantmerge &&
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
593 ln -s $input_data.quants ${counter}.quantmerge/quant.sf &&
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
594 #end for
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
595 salmon quantmerge
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
596 --quants *.quantmerge
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
597 --names
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
598 #for $counter, $input_data in enumerate($quantfiles):
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
599 #if $input_data.names and re.sub(' ', '', '$input_data.names') != '':
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
600 '${input_data.names}'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
601 #else:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
602 #set $identifier=re.sub('[^\w\-\s]', '_', str($input_data.quants.element_identifier))
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
603 "$identifier"
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
604 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
605 #end for
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
606 --column '${column}'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
607 ${genes}
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
608 #if $missing:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
609 --missing '${missing}'
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
610 #end if
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
611 -o qmergeout.tab
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
612 ]]>
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
613 </token>
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
614 <token name="@salmonhelp@"><![CDATA[
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
615 Salmon is a lightweight method for quantifying transcript abundance from RNA–seq reads, combining a dual-phase parallel inference algorithm and feature-rich bias models with an ultra-fast read mapping procedure.
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
616
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
617 The salmon package contains 4 tools:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
618
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
619 * Index: creates a salmon index
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
620
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
621 * Quant: quantifies a sample (Reads or mapping-based)
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
622
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
623 * Alevin: Single-cell analysis
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
624
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
625 * Quantmerge: Merges multiple quantifications into a single file
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
626
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
627 Galaxy divides these four into three separate tools in the IUC toolshed:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
628
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
629 * Salmon quant
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
630
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
631 * Salmon quantmerge
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
632
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
633 * Alevin
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
634 ]]>
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
635 </token>
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
636 <token name="@alevinhelp@"><![CDATA[
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
637 Alevin is a tool — integrated with the salmon software — that introduces a family of algorithms for quantification and analysis of 3’ tagged-end single-cell sequencing data. Currently alevin supports the following two major droplet based single-cell protocols:
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
638
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
639 * Drop-seq
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
640
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
641 * 10x-Chromium v1/2/3
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
642
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
643 Alevin works under the same indexing scheme (as salmon) for the reference, and consumes the set of FASTA/Q files(s) containing the Cellular Barcode(CB) + Unique Molecule identifier (UMI) in one read file and the read sequence in the other. Given just the transcriptome and the raw read files, alevin generates a cell-by-gene count matrix (in a fraction of the time compared to other tools).
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
644
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
645 Alevin works in two phases. In the first phase it quickly parses the read file containing the CB and UMI information to generate the frequency distribution of all the observed CBs, and creates a lightweight data-structure for fast-look up and correction of the CB. In the second round, alevin utilizes the read-sequences contained in the files to map the reads to the transcriptome, identify potential PCR/sequencing errors in the UMIs, and performs hybrid de-duplication while accounting for UMI collisions. Finally, a post-abundance estimation CB whitelisting procedure is done and a cell-by-gene count matrix is generated.
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
646
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
647 For further information regarding the tool and its optional parameters, visit the `Alevin <https://salmon.readthedocs.io/en/latest/alevin.html?highlight=alevin>`__ and `Salmon <https://salmon.readthedocs.io/en/latest/index.html>`__ wikis.
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
648 ]]>
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
649 </token>
4de6e2e40c7a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
650 </macros>