annotate macros.xml @ 4:85b3dc9b6830 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
author bgruening
date Mon, 13 Jul 2020 17:14:25 -0400
parents f6e3a10a88e5
children 88c07fc4024c
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1 <macros>
4
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2 <token name="@VERSION@">1.3.0</token>
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3 <token name="@GALAXY_VERSION@">galaxy0</token>
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4 <token name="@IDX_VERSION@">q7</token>
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5 <xml name="requirements">
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6 <requirements>
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7 <requirement type="package" version="@VERSION@">salmon</requirement>
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8 <requirement type="package" version="1.3">seqtk</requirement>
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9 <requirement type="package" version="1.10">samtools</requirement>
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10 <requirement type="package" version="0.2.0">vpolo</requirement>
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11 <requirement type="package" version="1.0.3">pandas</requirement>
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12 <requirement type="package" version="1.4.1">scipy</requirement>
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13 </requirements>
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14 </xml>
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15 <xml name="stranded">
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16 <param name="strandedness" type="select" label="Specify the strandedness of the reads">
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17 <option value="U" selected="True">Not stranded (U)</option>
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18 <option value="SF">read comes from the forward strand (SF)</option>
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19 <option value="SR">read comes from the reverse strand (SR)</option>
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20 </param>
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21 </xml>
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22 <xml name="orient">
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23 <param name="orientation" type="select" label="Relative orientation of reads within a pair">
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24 <option value="M">Mates are oriented in the same direction (M = matching)</option>
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25 <option value="O">Mates are oriented away from each other (O = outward)</option>
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26 <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option>
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27 </param>
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28 </xml>
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29 <xml name="index">
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30 <conditional name="refTranscriptSource">
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31 <param name="TranscriptSource" type="select" label="Select a reference transcriptome from your history or use a built-in index?"
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32 help="Built-ins were indexed using default options">
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33 <option value="indexed">Use a built-in index</option>
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34 <option value="history" selected="True">Use one from the history</option>
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35 </param>
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36 <when value="indexed">
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37 <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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38 <options from_data_table="salmon_indexes_versioned">
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39 <filter type="sort_by" column="2"/>
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40 <filter type="static_value" column="4" value="@IDX_VERSION@" />
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41 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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42 </options>
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43 </param>
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44 </when> <!-- build-in -->
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45 <when value="history">
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46 <section name="s_index" title="Salmon index" expanded="true">
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47 <param name="fasta" type="data" format="fasta" label="Transcripts fasta file"/>
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48 <param name="kmer" type="integer" value="31" label="Kmer length"/>
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49 <param name="phash" type="boolean" label="Perfect Hash" truevalue="--perfectHash" falsevalue="" checked="false"
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50 help="Build the index using a perfect hash rather than a dense hash. This will require less memory (especially during quantification), but will take longer to construct"/>
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51 </section>
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52 </when>
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53 </conditional>
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54 </xml>
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55 <xml name="reads">
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56 <section name="input" title="Data input" expanded="True">
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57 <conditional name="single_or_paired">
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58 <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?">
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59 <option value="single">Single-end</option>
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60 <option value="paired">Paired-end</option>
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61 <option value="paired_collection">Paired-end Dataset Collection</option>
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62 <option value="paired_interleaved">Paired-end data from single interleaved dataset</option>
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63 </param>
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64 <when value="single">
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65 <param name="input_singles" type="data" format="fastq,fasta,fastq.gz,fastq.bz2" label="FASTQ/FASTA file" help="FASTQ file." />
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66 <expand macro="stranded"/>
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67 </when>
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68 <when value="paired">
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69 <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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70 <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." />
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71 <expand macro="orient"/>
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72 <expand macro="stranded"/>
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73 </when>
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74 <when value="paired_collection">
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75 <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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76 <expand macro="orient"/>
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77 <expand macro="stranded"/>
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78 </when>
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79 <when value="paired_interleaved">
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80 <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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81 <expand macro="orient"/>
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82 <expand macro="stranded"/>
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83 </when>
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84 </conditional>
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85 </section>
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86 <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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87 <option value="quasi" selected="True">quasi</option>
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88 </param>
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89 <!--Salmon quant type select: reads-based or alignment-based-->
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90 <param name="discardOrphansQuasi" type="boolean" truevalue="--discardOrphansQuasi" falsevalue="" checked="False"
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91 label="Discard orphan quasi"
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92 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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93 <conditional name="validmap">
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94 <param name="validateMappings" type="boolean" truevalue="--validateMappings" falsevalue="" checked="False"
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95 label="Validate mappings"
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96 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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97 <when value="--validateMappings">
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98 <param name="minScoreFraction" type="float" value="0.65" min="0.0" max="0.99"
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99 label="Min Score Fraction"
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100 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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101 <param name="maxMMPExtension" type="integer" optional="True"
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102 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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103 <param name="matchScore" argument="--ma" type="integer" value="2"
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104 label="Match Score"
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105 help="The value given to a match between read and reference nucleotides in an alignment."/>
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106 <param name="mismatchPenalty" argument="--mp" type="integer" value="4"
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107 label="Mismatch Penalty"
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108 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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109 <param name="gapOpenPenalty" argument="--go" type="integer" value="5"
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110 label="Gap Open Penalty"
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111 help="The value given to a gap opening in an alignment."/>
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112 <param name="gapExtensionPenalty" argument="--ge" type="integer" value="3"
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113 label="Gap Extension Penalty"
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114 help="The value given to a gap extension in an alignment."/>
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115 <param name="mimicBT2" type="boolean" truevalue="--mimicBT2" falsevalue="" checked="False"
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116 label="Mimic Bowtie 2"
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117 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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118 <param name="mimicStrictBT2" type="boolean" truevalue="--mimicStrictBT2" falsevalue="" checked="False"
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119 label="Mimic Strict Bowtie 2"
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120 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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121 <param name="hardFilter" type="boolean" truevalue="--hardFilter" falsevalue="" checked="False"
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122 label="Hard Filter"
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123 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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124 </when>
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125 <when value=""/>
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126 </conditional>
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127 <param name="consensusSlack" type="integer" optional="True" value="0"
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128 label="Consensus Slack"
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129 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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130 <param name="dovetail" label="Allow Dovetail" type="boolean" truevalue="--allowDovetail" falsevalue="" checked="False" help="Allow dovetail mappings"/>
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131 <param name="recoverOrphans" label="Recover Orphans" type="boolean" truevalue="--recoverOrphans" falsevalue="" checked="False"
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132 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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133 <param name="writeMappings" type="boolean" truevalue="--writeMappings=./output/samout.sam" falsevalue="" checked="False"
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134 label="Write Mappings to Bam File"
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135 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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136 <param name="consistentHits" type="boolean" truevalue="--consistentHits" falsevalue="" checked="False"
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137 label="Consistent Hits"
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138 help="Force hits gathered during quasi-mapping to be 'consistent' (i.e. co-linear and approximately the right distance apart)."/>
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139 <param name="quasiCoverage" type="integer" optional="True" label="Quasi Coverage"
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140 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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141 </xml>
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142 <xml name="align">
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143 <param name="afile" type="data" format="bam" label="Alignment file"/>
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144 <param name="transcript" type="data" format="fasta,fa" label="Transcript file"/>
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145 <expand macro="stranded"/>
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146 <param name="discardOrphans" type="boolean" truevalue="--discardOrphans" falsevalue="" checked="False"
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147 label="Discard orphans"
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148 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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149 <param name="noErrorModel" type="boolean" truevalue="--noErrorModel" falsevalue="" checked="False"
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150 label="No Error Model"
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151 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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152 <param name="numErrorBins" type="integer" optional="True" value="6"
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153 label="Number of Error Bins"
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154 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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155 <param name="sampleOut" type="boolean" truevalue="--sampleOut" falsevalue="" checked="False"
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156 label="Sample out"
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157 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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158 <param name="sampleUnaligned" type="boolean" truevalue="--sampleUnaligned" falsevalue="" checked="False"
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159 label="Sample unaligned"
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160 help="In addition to sampling the aligned reads, also write the un-aligned reads to 'postSample.bam'."/>
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161 <param name="gencode" type="boolean" truevalue="--gencode" falsevalue="" checked="False"
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162 label="Gencode"
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163 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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164 </xml>
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165 <xml name="quantboth">
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166 <param name="geneMap" type="data" format="tabular,gff,gtf" optional="True"
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167 label="File containing a mapping of transcripts to genes"
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168 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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169 <param name="seqBias" type="boolean" truevalue="--seqBias" falsevalue="" checked="False"
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170 label="Perform sequence-specific bias correction"/>
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171 <param name="gcBias" type="boolean" truevalue="--gcBias" falsevalue="" checked="False"
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172 label="Perform fragment GC bias correction"/>
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173 <param name="incompatPrior" type="float" optional="True" min="0.0" max="1" value="0"
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174 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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175 <param name="meta" type="boolean" truevalue="--meta" falsevalue="" checked="False"
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176 label="Meta"
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177 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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178 <!--Salmon quant advanced options: available to both kinds of quant-->
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179 <section name="adv" title="Additional Options">
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180 <param name="skipQuant" type="boolean" truevalue="--skipQuant" falsevalue="" checked="False"
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181 label="skipQuant" help="Skip performing the actual transcript quantification (including any Gibbs sampling or bootstrapping)."/>
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182 <param name="dumpEq" type="boolean" truevalue="--dumpEq" falsevalue="" checked="False"
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183 label="Dump equivalence class counts"
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184 help="Dump the equivalence class counts that were computed during quasi-mapping."/>
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185 <param name="dumpEqWeights" type="boolean" truevalue="--dumpEqWeights" falsevalue="" checked="False"
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186 label="Dump equivalence class counts including rich weights"
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187 help="Includes 'rich' equivlance class weights in the output when equivalence class information is being dumped to file."/>
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188 <param name="minAssignedFrags" type="integer" optional="True" label="Minimum assigned fragments"
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189 help="The minimum number of fragments that must be assigned to the transcriptome for quantification to proceed."/>
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190 <param name="biasSpeedSamp" type="integer" value="5" optional="True"
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191 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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192 <param name="fldMax" type="integer" value="1000" optional="True"
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193 label="The maximum fragment length to consider when building the empirical distribution."/>
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194 <param name="fldMean" type="integer" value="250" optional="True"
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195 label="The mean used in the fragment length distribution prior"
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196 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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197 <param name="fldSD" type="integer" value="25" optional="True"
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198 label="Standard deviation"
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199 help="The standard deviation used in the fragment length distribution prior."/>
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200 <param name="forgettingFactor" type="float" value="0.65000000000000002" optional="True"
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201 label="The forgetting factor used in the online learning schedule."
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202 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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203 <param name="initUniform" type="boolean" truevalue="--initUniform" falsevalue="" checked="False"
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204 label="Initialization with uniform parameters"
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205 help="initialize the offline inference with uniform parameters, rather than seeding with online parameters." />
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206 <param name="maxReadOcc" type="integer" value="100" optional="True"
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207 label="Maximal read mapping occurence"
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208 help="Reads mapping to more than this many places won't be considered."/>
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209 <param name="noLengthCorrection" type="boolean" truevalue="--noLengthCorrection" falsevalue=""
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210 label="No length correction"
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211 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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212 <param name="noEffectiveLengthCorrection" type="boolean" truevalue="--noEffectiveLengthCorrection" falsevalue="" checked="False"
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213 label="Disable effective length correction"
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214 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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215 <param name="noFragLengthDist" type="boolean" truevalue="--noFragLengthDist" falsevalue="" checked="False"
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216 label="Ignore fragment length distribution"
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217 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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218 <param name="noBiasLengthThreshold" type="boolean" truevalue="--noBiasLengthThreshold" falsevalue="" checked="False"
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219 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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220 help="This can increase the precision of bias correction, but harm robustness. The default correction applies a threshold." />
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221 <param name="numBiasSamples" type="integer" value="2000000" optional="True"
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222 label="Number of fragment mappings to use when learning the sequence-specific bias model."/>
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223 <param name="numAuxModelSamples" type="integer" value="5000000" optional="True"
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224 label="The first numAuxModelSamples are used to train the auxiliary model parameters."
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225 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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226 <param name="numPreAuxModelSamples" type="integer" value="5000" optional="True"
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227 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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228 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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229 <param name="useEM" type="boolean" truevalue="--useEM" falsevalue="" checked="False"
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230 label="Use the traditional EM algorithm for optimization in the batch passes."
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231 help=""/>
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232 <param name="rangeFactorizationBins" type="integer" value="0" label="Range of factorization bins"
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233 help="Factorizes the likelihood used in quantification by adopting a new notionof 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."/>
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234 <param name="numGibbsSamples" type="integer" value="0" optional="True"
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235 label="Number of Gibbs sampling rounds to perform."
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236 help="" />
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237 <param name="noGammaDraw" type="boolean" truevalue="--noGammaDraw" falsevalue="" checked="False"
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238 label="No gamma draw"
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239 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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240 <param name="numBootstraps" type="integer" value="0" optional="True"
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241 label="Number of bootstrap samples to generate. Note: This is mutually exclusive with Gibbs sampling."
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242 help="" />
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243 <param name="bootstrapReproject" type="boolean" truevalue="--bootstrapReproject" falsevalue="" checked="False"
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244 label="Bootstrap reproject"
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245 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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246 <param name="thinningFactor" type="integer" value="16" optional="true" label="Thinning factor"
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247 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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248 <param name="perTranscriptPrior" type="boolean" truevalue="--perTranscriptPrior" falsevalue="" checked="False"
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249 label="The prior will be interpreted as a transcript-level prior."
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250 help="either the default or the argument provided via --vbPrior" />
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251 <param name="sigDigits" type="integer" value="3"
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252 label="Significant Digits"
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253 help="The number of significant digits to write when outputting the EffectiveLength and NumReads columns."/>
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254 <param name="vbPrior" type="float" value="1.0000000000000001e-05" optional="True"
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255 label="The prior that will be used in the VBEM algorithm."
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256 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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257 <param name="writeOrphanLinks" type="boolean" truevalue="--writeOrphanLinks" falsevalue="" checked="False" label="Write orphan links"
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258 help="Write the transcripts that are linked by orphaned reads."/>
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259 <param name="writeUnmappedNames" type="boolean" truevalue="--writeUnmappedNames" falsevalue="" checked="False"
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260 label="Write the names of un-mapped reads to the file unmapped_names.txt."
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261 help=""/>
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262 </section>
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263 </xml>
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264 <xml name="quantmerge">
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265 <repeat name="quantfiles" title="Quant file and names">
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266 <param name="quants" type="data" format="tsv,tabular"
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267 label="Salmon quant tabular output files"/>
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268 <param name="names" type="text" label="One-word sample names" optional="True"/>
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269 </repeat>
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270 <param name="column" type="select" label="Columns"
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271 help="Name of columns that will be merged in the output file">
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272 <option value="len" selected="True">Length</option>
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273 <option value="elen">Effective Length</option>
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274 <option value="tpm">Transcripts per Million</option>
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275 <option value="numreads">NumReads</option>
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276 </param>
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277 <param name="genes" type="boolean" truevalue="--genes" falsevalue="" checked="False"
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278 label="Genes" help="Use gene quantifications instead of transcript"/>
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279 <param name="missing" type="integer" label="Missing" optional="True" help="The value of missing values"/>
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280 </xml>
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281 <xml name="citations">
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282 <citations>
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283 <citation type="doi">10.1186/s13059-019-1670-y</citation>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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284 <citation type="doi">10.1038/nmeth.4197</citation>
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285 </citations>
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286 </xml>
3
f6e3a10a88e5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 30fe16f7d786e4b0c43b8333853fc56c59f6c664"
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287 <token name="@bam_sort@"><![CDATA[samtools sort -@ \${GALAXY_SLOTS} --output-fmt=BAM -o ./output/bamout.bam]]></token>
0
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288 <token name="@indexing@"><![CDATA[
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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289 mkdir ./index &&
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290 mkdir ./output &&
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291 #if $quant_type.refTranscriptSource.TranscriptSource != "indexed":
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292 salmon index -i ./index
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293 --kmerLen '${quant_type.refTranscriptSource.s_index.kmer}'
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294 --gencode
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295 --transcripts '${quant_type.refTranscriptSource.s_index.fasta}'
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296 &&
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297 #set $index_path = './index'
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298 #else
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299 #set $index_path = $quant_type.refTranscriptSource.index.fields.path
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300 #end if
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301 ]]>
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302 </token>
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303 <token name="@salreads@"><![CDATA[
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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304 #set compressed = 'no'
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305 #if $quant_type.input.single_or_paired.single_or_paired_opts == 'single':
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306 #if $quant_type.input.single_or_paired.input_singles.ext == 'fasta':
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307 #set $ext = 'fasta'
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308 #else:
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309 #if $quant_type.input.single_or_paired.input_singles.is_of_type("fastq.gz", "fastqsanger.gz"):
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310 #set compressed = 'GZ'
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311 #else if $quant_type.input.single_or_paired.input_singles.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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312 #set compressed = 'BZ2'
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313 #end if
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314 #set $ext = 'fastq'
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315 #end if
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316 ln -s $quant_type.input.single_or_paired.input_singles ./single.$ext &&
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317 #else if $quant_type.input.single_or_paired.single_or_paired_opts == 'paired':
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318 #if $quant_type.input.single_or_paired.input_mate1.ext == 'fasta':
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319 #set $ext = 'fasta'
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320 #else:
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321 #if $quant_type.input.single_or_paired.input_mate1.is_of_type("fastq.gz", "fastqsanger.gz"):
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322 #set compressed = 'GZ'
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323 #else if $quant_type.input.single_or_paired.input_mate1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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324 #set compressed = 'BZ2'
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325 #end if
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326 #set $ext = 'fastq'
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327 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
328 ln -s $quant_type.input.single_or_paired.input_mate1 ./mate1.$ext &&
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
329 ln -s $quant_type.input.single_or_paired.input_mate2 ./mate2.$ext &&
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
330 #else if $quant_type.input.single_or_paired.single_or_paired_opts == 'paired_collection':
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
331 #if $quant_type.input.single_or_paired.input_1.forward.ext == 'fasta':
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
332 #set $ext = 'fasta'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
333 #else:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
334 #if $quant_type.input.single_or_paired.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
335 #set compressed = 'GZ'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
336 #else if $quant_type.input.single_or_paired.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
337 #set compressed = 'BZ2'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
338 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
339 #set $ext = 'fastq'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
340 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
341 ln -s '${quant_type.input.single_or_paired.input_1.forward}' ./mate1.$ext &&
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
342 ln -s '${quant_type.input.single_or_paired.input_1.reverse}' ./mate2.$ext &&
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
343 #else if '$quant_type.input.single_or_paired.single_or_paired_opts' == 'paired_interleaved':
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
344 #if $quant_type.input.single_or_paired.input_1.ext == 'fasta':
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
345 #set $ext = 'fasta'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
346 #else:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
347 #if $quant_type.input.single_or_paired.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
348 #set compressed = 'GZ'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
349 #else if $quant_type.input.single_or_paired.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
350 #set compressed = 'BZ2'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
351 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
352 #set $ext = 'fastq'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
353 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
354 ln -s '$quant_type.input.single_or_paired.input_1' ./mate1.$ext &&
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
355 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
356 #if $geneMap:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
357 ln -s '$geneMap' ./geneMap.${geneMap.ext} &&
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
358 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
359
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
360 salmon quant
4
85b3dc9b6830 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
bgruening
parents: 3
diff changeset
361 --index '$index_path'
0
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
362 #if $quant_type.input.single_or_paired.single_or_paired_opts == 'single':
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
363 --libType ${quant_type.input.single_or_paired.strandedness}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
364 #if $compressed == 'GZ':
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
365 --unmatedReads <(zcat < ./single.$ext)
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
366 #else if $compressed == 'BZ2':
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
367 --unmatedReads <(bzcat < ./single.$ext)
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
368 #else:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
369 --unmatedReads ./single.$ext
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
370 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
371 #else:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
372 --libType '${quant_type.input.single_or_paired.orientation}${quant_type.input.single_or_paired.strandedness}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
373 #if $quant_type.input.single_or_paired.single_or_paired_opts == 'paired_interleaved':
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
374 #if $compressed == 'BZ2':
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
375 --mates1 <(bzcat < ./mate1.$ext | seqtk seq -1)
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
376 --mates2 <(bzcat < ./mate1.$ext | seqtk seq -2)
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
377 #else:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
378 --mates1 <(seqtk seq -1 ./mate1.$ext)
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
379 --mates2 <(seqtk seq -2 ./mate1.$ext)
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
380 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
381 #else:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
382 #if $compressed == 'GZ':
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
383 --mates1 <(zcat < ./mate1.$ext)
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
384 --mates2 <(zcat < ./mate2.$ext)
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
385 #else if $compressed == 'BZ2':
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
386 --mates1 <(bzcat < ./mate1.$ext)
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
387 --mates2 <(bzcat < ./mate2.$ext)
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
388 #else:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
389 --mates1 ./mate1.$ext
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
390 --mates2 ./mate2.$ext
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
391 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
392 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
393 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
394 --threads "\${GALAXY_SLOTS:-4}"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
395 ${quant_type.discardOrphansQuasi}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
396 ${quant_type.validmap.validateMappings}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
397 #if $quant_type.validmap.validateMappings:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
398 #if $quant_type.validmap.minScoreFraction:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
399 --minScoreFraction '${quant_type.validmap.minScoreFraction}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
400 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
401 #if $quant_type.validmap.maxMMPExtension:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
402 --maxMMPExtension '${quant_type.validmap.maxMMPExtension}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
403 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
404 #if $quant_type.validmap.matchScore:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
405 --ma '${$quant_type.validmap.matchScore}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
406 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
407 #if $quant_type.validmap.mismatchPenalty:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
408 --mp '${$quant_type.validmap.mismatchPenalty}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
409 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
410 #if $quant_type.validmap.gapOpenPenalty:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
411 --go '${$quant_type.validmap.gapOpenPenalty}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
412 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
413 #if $quant_type.validmap.gapExtensionPenalty:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
414 --ge '${$quant_type.validmap.gapExtensionPenalty}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
415 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
416 ${$quant_type.validmap.mimicBT2}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
417 ${$quant_type.validmap.mimicStrictBT2}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
418 ${$quant_type.validmap.hardFilter}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
419 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
420 #if $quant_type.consensusSlack:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
421 --consensusSlack '${quant_type.consensusSlack}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
422 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
423 ${quant_type.dovetail}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
424 ${quant_type.recoverOrphans}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
425 ${quant_type.writeMappings}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
426 ${quant_type.consistentHits}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
427 #if $quant_type.quasiCoverage:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
428 --quasiCoverage '${quant_type.quasiCoverage}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
429 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
430 ]]>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
431 </token>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
432 <token name="@salalign@"><![CDATA[
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
433 #if $geneMap:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
434 ln -s "$geneMap" ./geneMap.${geneMap.ext} &&
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
435 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
436 salmon quant
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
437 -t '${quant_type.transcript}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
438 -l '${quant_type.strandedness}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
439 -a '${quant_type.afile}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
440 --threads "\${GALAXY_SLOTS:-4}"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
441 ${quant_type.discardOrphans}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
442 ${quant_type.noErrorModel}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
443 #if $quant_type.numErrorBins:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
444 --numErrorBins '${quant_type.numErrorBins}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
445 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
446 ${quant_type.sampleOut}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
447 ${quant_type.sampleUnaligned}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
448 ${quant_type.gencode}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
449 ]]>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
450 </token>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
451 <token name="@salquant@"><![CDATA[
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
452 #if $geneMap:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
453 --geneMap ./geneMap.${geneMap.ext}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
454 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
455
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
456 ##Further basic options##
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
457
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
458 ${seqBias}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
459 ${gcBias}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
460 --incompatPrior '${incompatPrior}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
461 ${meta}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
462
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
463 ##Advanced options##
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
464
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
465 ${adv.skipQuant}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
466 ${adv.dumpEq}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
467 ${adv.dumpEqWeights}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
468 #if $adv.minAssignedFrags:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
469 --minAssignedFrags '${adv.minAssignedFrags}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
470 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
471 #if $adv.biasSpeedSamp:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
472 --biasSpeedSamp '${adv.biasSpeedSamp}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
473 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
474 #if $adv.fldMax:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
475 --fldMax '${adv.fldMax}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
476 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
477 #if $adv.fldMean:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
478 --fldMean '${adv.fldMean}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
479 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
480 #if $adv.fldSD:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
481 --fldSD '${adv.fldSD}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
482 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
483 #if $adv.forgettingFactor:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
484 --forgettingFactor '${adv.forgettingFactor}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
485 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
486 ${adv.initUniform}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
487 #if str($adv.maxReadOcc):
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
488 --maxReadOcc '${adv.maxReadOcc}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
489 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
490 ${adv.noLengthCorrection}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
491 ${adv.noEffectiveLengthCorrection}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
492 ${adv.noFragLengthDist}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
493 ${adv.noBiasLengthThreshold}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
494 #if str($adv.numBiasSamples):
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
495 --numBiasSamples '${adv.numBiasSamples}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
496 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
497 #if str($adv.numAuxModelSamples):
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
498 --numAuxModelSamples '${adv.numAuxModelSamples}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
499 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
500 #if str($adv.numPreAuxModelSamples):
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
501 --numPreAuxModelSamples '${adv.numPreAuxModelSamples}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
502 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
503 ${adv.useEM}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
504 #if $adv.rangeFactorizationBins:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
505 --rangeFactorizationBins '${adv.rangeFactorizationBins}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
506 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
507 #if str($adv.numGibbsSamples):
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
508 --numGibbsSamples '${adv.numGibbsSamples}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
509 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
510 ${adv.noGammaDraw}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
511 #if str($adv.numBootstraps):
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
512 --numBootstraps '${adv.numBootstraps}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
513 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
514 ${adv.bootstrapReproject}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
515 #if $adv.thinningFactor:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
516 --thinningFactor '${adv.thinningFactor}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
517 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
518 ${adv.perTranscriptPrior}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
519 --sigDigits '${adv.sigDigits}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
520 #if $adv.vbPrior:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
521 --vbPrior '${adv.vbPrior}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
522 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
523 ${adv.writeOrphanLinks}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
524 ${adv.writeUnmappedNames}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
525 -o ./output
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
526 ]]>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
527 </token>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
528 <token name="@qmerge@"><![CDATA[
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
529 #import re
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
530
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
531 #for $counter, $input_data in enumerate($quantfiles):
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
532 rank_of_series=$counter
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
533 mkdir ${counter}.quantmerge &&
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
534 ln -s $input_data.quants ${counter}.quantmerge/quant.sf &&
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
535 #end for
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
536 salmon quantmerge
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
537 --quants *.quantmerge
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
538 --names
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
539 #for $counter, $input_data in enumerate($quantfiles):
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
540 #if $input_data.names and re.sub(' ', '', '$input_data.names') != '':
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
541 '${input_data.names}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
542 #else:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
543 #set $identifier=re.sub('[^\w\-\s]', '_', str($input_data.quants.element_identifier))
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
544 "$identifier"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
545 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
546 #end for
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
547 --column '${column}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
548 ${genes}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
549 #if $missing:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
550 --missing '${missing}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
551 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
552 -o qmergeout.tab
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
553 ]]>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
554 </token>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
555 <token name="@salmonhelp@"><![CDATA[
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
556 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.
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
557
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
558 The salmon package contains 4 tools:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
559
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
560 * Index: creates a salmon index
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
561
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
562 * Quant: quantifies a sample (Reads or mapping-based)
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
563
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
564 * Alevin: Single-cell analysis
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
565
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
566 * Quantmerge: Merges multiple quantifications into a single file
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
567
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
568 Galaxy divides these four into three separate tools in the IUC toolshed:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
569
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
570 * Salmon quant
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
571
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
572 * Salmon quantmerge
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
573
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
574 * Alevin
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
575 ]]>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
576 </token>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
577 <token name="@alevinhelp@"><![CDATA[
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
578 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:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
579
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
580 * Drop-seq
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
581
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
582 * 10x-Chromium v1/2/3
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
583
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
584 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).
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
585
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
586 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.
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
587
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
588 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.
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
589 ]]>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
590 </token>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
591 </macros>