annotate alevin.xml @ 16:b0fe3e482cb7 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 6954ddebecfe9f0975f2c7e29193e4c99c550514
author bgruening
date Mon, 28 Oct 2024 17:50:35 +0000
parents c9944a2600f1
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
11
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
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1 <tool id="alevin" name="Alevin" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE_VERSION@">
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2 <description>Quantification and analysis of 3-prime tagged-end single-cell sequencing data</description>
0
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a
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6 <expand macro="xrefs"/>
0
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 mkdir ./index
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10 && mkdir ./output
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11 #if $refTranscriptSource.TranscriptSource != "indexed":
0
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12 && salmon index -i ./index
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13 --kmerLen '${refTranscriptSource.s_index.kmer}'
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14 --gencode
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15 --transcripts '${refTranscriptSource.s_index.fasta}'
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16 #set $index_path = './index'
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17 #else
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18 #set $index_path = $refTranscriptSource.index.fields.path
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19 #end if
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20 #if $pairstraight.readselect == 'paired':
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21 #if $pairstraight.file1.is_of_type("fastq.gz"):
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22 && cp '${pairstraight.file1}' ./mate1.fastq.gz
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23 && gunzip ./mate1.fastq.gz
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24 && cp '${pairstraight.file2}' ./mate2.fastq.gz
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25 && gunzip ./mate2.fastq.gz
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26 #else if $pairstraight.file1.is_of_type("fastq.bz2"):
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27 && cp '${pairstraight.file1}' ./mate1.fastq.bz2
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28 && bzip2 -d ./mate1.fastq.bz2
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29 && cp '${pairstraight.file2}' ./mate2.fastq.bz2
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30 && bzip2 -d ./mate2.fastq.bz2
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31 #else:
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32 && ln -s '${pairstraight.file1}' ./mate1.fastq
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33 && ln -s '${pairstraight.file2}' ./mate2.fastq
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34 #end if
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35 #else:
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36 #if $pairstraight.unmatedreads.is_of_type("fastq.gz"):
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37 && cp '${pairstraight.unmatedreads}' ./unmate.fastq.gz
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38 && gunzip ./unmate.fastq.gz
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39 #else if $pairstraight.unmatedreads.is_of_type("fastq.bz2"):
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40 && cp '${pairstraight.unmatedreads}' ./unmate.fastq.bz2
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41 && bzip2 -d unmate.fastq.bz2
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42 #else:
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43 && ln -s '${pairstraight.unmatedreads}' ./unmate.fastq
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44 #end if
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45 #end if
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46
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47 && ln -s '${tgmap}' ./alevinmap.tsv
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48 && salmon alevin -l
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49 #if $pairstraight.readselect == 'paired':
10
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50 #if $pairstraight.libtype.strandedness == 'A'
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51 A
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52 #else
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53 ${pairstraight.libtype.orientation}${pairstraight.libtype.strandedness}
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54 #end if
0
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55 -i $index_path
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56 -1 ./mate1.fastq
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57 -2 ./mate2.fastq
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58 #else:
10
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59 '${pairstraight.libtype.strandedness}'
0
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60 -i $index_path
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61 -r zcat ./unmate.fastq
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62 #end if
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63 -o ./output
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64 -p "\${GALAXY_SLOTS:-4}"
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65 ${protocol_cond.protocol}
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66 #if $protocol_cond.protocol == '--indropV2'
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67 --w1 '${protocol_cond.w1}'
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68 #end if
0
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69 --tgMap ./alevinmap.tsv
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70 #if $whitelist:
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71 --whitelist '${optional.whitelist}'
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72 #end if
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73 #if $optional.numCellBootstraps:
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74 --numCellBootstraps '${optional.numCellBootstraps}'
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75 #end if
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76 #if $optional.forceCells:
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77 --forceCells '${optional.forceCells}'
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78 #end if
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79 #if $optional.expectCells:
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80 --expectCells '${optional.expectCells}'
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81 #end if
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82 #if $optional.mrna:
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83 --mrna '${optional.mrna}'
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84 #end if
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85 #if $optional.rrna:
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86 --rrna '${optional.rrna}'
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87 #end if
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88 #if $optional.keepCBFraction:
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89 --keepCBFraction '${optional.keepCBFraction}'
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90 #end if
2
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91 ${optional.noDedup}
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92 #if 'dumpBfh' in $output_files:
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93 --dumpBfh
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94 #end if
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95 #if 'dumpFeatures' in $output_files:
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96 --dumpFeatures
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97 #end if
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98 #if 'dumpUmiGraph' in $output_files:
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99 --dumpUmiGraph
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100 #end if
0
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101 ${optional.dumpMtx}
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102 #if $optional.maxNumBarcodes:
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103 --maxNumBarcodes '${optional.maxNumBarcodes}'
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104 #end if
4
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105 #if $optional.freqThreshold:
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106 --freqThreshold '${optional.freqThreshold}'
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107 #end if
11
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108 ## && gunzip output/alevin/quants_tier_mat.gz -> the output is binary file
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109 #if $optional.dumpMtx != "--dumpMtx":
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110 && python '$__tool_directory__/vpolo_convert.py' -m
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111 #else:
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112 && gunzip output/alevin/quants_mat.mtx.gz
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113 #end if
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114 #if 'dumpUmiGraph' in $output_files:
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115 && python '$__tool_directory__/vpolo_convert.py' -u
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116 && sh '$__tool_directory__/umiout.sh'
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117 #end if
11
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118 ## those gzip file include binary datasets
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119 ## #if $optional.numCellBootstraps:
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120 ## && gunzip output/alevin/quants_mean_mat.gz
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121 ## && gunzip output/alevin/quants_var_mat.gz
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122 ## #end if
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123 #if 'auxiliar_info' in $output_files
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124 && tar -zcvf aux_info.tar.gz output/aux_info
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125 #end if
0
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126 ]]>
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127 </command>
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128 <inputs>
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129 <expand macro="index"/>
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130 <conditional name="pairstraight">
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131 <param name="readselect" label="Single or paired-end reads?" type="select">
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132 <option value="paired">Paired-end</option>
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133 <option value="unmated">Single-end</option>
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134 </param>
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135 <when value="paired">
11
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136 <param name="file1" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" label="Mate pair 1" help="CB+UMI raw sequence file(s)"/>
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137 <param name="file2" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" label="Mate pair 2" help="Read-sequence file(s)"/>
10
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138 <expand macro="stranded_pe"/>
0
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139 </when>
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140 <when value="unmated">
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141 <param name="unmatedreads" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" label="Unmated reads files"/>
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142 <expand macro="stranded_se"/>
0
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143 </when>
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144 </conditional>
11
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145 <conditional name="protocol_cond">
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146 <param name="protocol" type="select" label="Type of single-cell protocol" help="In cases where single-cell protocol supports variable length cellbarcodes, alevin adds nucleotide padding to make the lengths uniform. Furthermore, the padding scheme ensures that there are no collisions added in the process.">
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147 <option value="--dropseq">DropSeq Single Cell protocol</option>
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148 <option value="--chromium">10x chromium v2 Single Cell protocol</option>
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149 <option value="--chromiumV3">10x chromium v3 Single Cell protocol</option>
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150 <option value="--gemcode">Gemcode v1 Single Cell protocol</option>
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151 <option value="--celseq">CEL-Seq Single Cell protocol</option>
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152 <option value="--celseq2">CEL-Seq2 Single Cell protocol</option>
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153 <option value="--sciseq3">Sci-RNA-seq3 protocol</option>
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154 <option value="--indropV2">InDrop v2 protocol</option>
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155 <option value="--splitSeqV1">SplitSeqV1 protocol</option>
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156 <option value="--splitSeqV2">SplitSeqV2 protocol</option>
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157 </param>
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158 <when value="--dropseq"/>
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159 <when value="--chromium"/>
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160 <when value="--chromiumV3"/>
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161 <when value="--gemcode"/>
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162 <when value="--celseq"/>
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163 <when value="--celseq2"/>
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164 <when value="--sciseq3"/>
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165 <when value="--indropV2">
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166 <param argument="--w1" type="text" value="" label="w1 adapters">
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167 <sanitizer invalid_char="">
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168 <valid initial="string.letters"/>
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169 </sanitizer>
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170 <validator type="regex">[ATGC]+</validator>
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171 </param>
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172 </when>
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173 <when value="--splitSeqV1"/>
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174 <when value="--splitSeqV2"/>
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175 </conditional>
0
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176 <param name="tgmap" type="data" format="tsv,tabular" label="Transcript to gene map file" help="Tsv with no header, containing two columns mapping each transcript present in the reference to the corresponding gene (the first column is a transcript and the second is the corresponding gene)."/>
11
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177 <param name="output_files" type="select" multiple="true" display="checkboxes" label="Extra output files">
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178 <option value="salmon_log">Salmon Quant log file</option>
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179 <option value="fragment_length">Observed fragment length distribution</option>
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180 <option value="auxiliar_info">Auxiliar info files</option>
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181 <option value="dumpUmiGraph">Per cell level parsimonious Umi graph (--dumpUmiGraph)</option>
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182 <option value="dumpFeatures">Features used by the CB classification and their counts at each cell level (--dumpFeatures)</option>
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183 <option value="dumpBfh">Full CB-EC-UMI-count data-structure (--dumpBfh)</option>
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184 <option value="commands">Commands info file</option>
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185 </param>
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186 <section name="optional" title="Advanced options" expanded="false">
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187 <param argument="--whitelist" type="data" format="tsv,tabular" optional="true" label="Whitelist file" help="Explicitly specify whitelist CP for cell detection and CB sequence correction. If not specified, putative CBs generated."/>
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188 <param argument="--noDedup" type="boolean" truevalue="--noDedup" falsevalue="" checked="false" label="Skip deduplication step" help="Causes pipeline to only perform CB correction, then maps the read-sequences to the transcriptome generating the interim data-structure of CB-EqClass-UMI-count. Used in parallel with --dumpBarcodeEq or --dumpBfh for the purposes of obtaining raw information or debugging."/>
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189 <param argument="--mrna" type="data" format="tsv" optional="true" label="Mito-RNA genes file" help="Single column tsv of mitochondrial genes which are to be used as a feature for CB whitelising naive Bayes classification."/>
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190 <param argument="--rrna" type="data" format="tsv" optional="true" label="Ribosomal RNA file" help="Single column tsv of ribosomal genes which are to be used as a feature for CB whitelising naive Bayes classification."/>
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191 <param argument="--dumpMtx" type="boolean" truevalue="--dumpMtx" falsevalue="" checked="false" label=" Dump cell v transcripts count matrix in MTX format" help="Converts the default binary format of alevin for gene-count matrix into a human readable mtx (matrix market exchange) sparse format."/>
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192 <param argument="--forceCells" type="integer" min="0" optional="true" label="Number of cells" help="Explicitly specify the number of cells."/>
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193 <param argument="--expectCells" type="integer" min="0" optional="true" label="Upper bound on expected number of cells" help="define a close upper bound on expected number of cells."/>
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194 <param argument="--numCellBootstraps" type="integer" min="0" value="0" optional="true" label="Generate mean and variance for cell x gene matrix by boostrap" help="Performs certain number of bootstrap and generate the mean and variance of the count matrix"/>
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195 <param argument="--minScoreFraction" type="float" optional="true" label="Minimum allowed score for a mapping" help="This value controls the minimum allowed score for a mapping to be considered valid. It matters only when --validateMappings has been passed to Salmon. The maximum possible score for a fragment is ms = read_len * ma (or ms = (left_read_len + right_read_len) * ma for paired-end reads).
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196 The argument to --minScoreFraction determines what fraction of the maximum score s a mapping must achieve to be potentially retained. For a minimum score fraction of f, only mappings with a score less than (f * s) will be kept. Mappings with lower scores will be considered as low-quality, and will be discarded."/>
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197 <param argument="--keepCBFraction" type="float" min="0" max="1" optional="true" label="Fraction of cellular barcodes to keep" help="Use 1 to quantify all"/>
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198 <param argument="--maxNumBarcodes" type="integer" min="0" value="100000" label="Maximum allowable limit to process the cell barcodes" help="Default: 100000"/>
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199 <param argument="--freqThreshold" type="integer" min="0" value="10" optional="true" label="Minimum frequency for a barcode to be considered" help="Default: 10"/>
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200 </section>
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201 </inputs>
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202 <outputs>
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203 <data name="quants_mat_tsv" label="${tool.name} on ${on_string}: per-cell gene-count matrix (tabular)" format="txt" from_work_dir="quants_mat.tsv">
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204 <filter>optional["dumpMtx"] is not True</filter>
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205 </data>
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206 <data name="quants_mat_mtx" label="${tool.name} on ${on_string}: per-cell gene-count matrix (MTX)" format="mtx" from_work_dir="output/alevin/quants_mat.mtx">
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207 <filter>optional["dumpMtx"]</filter>
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208 </data>
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209 <data name="quants_mat_gz" label="${tool.name} on ${on_string}: per-cell level gene-count matrix (binary)" format="gz" from_work_dir="output/alevin/quants_mat.gz"/>
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210 <data name="quants_mat_cols_txt" label="${tool.name} on ${on_string}: column headers (gene-ids)" format="txt" from_work_dir="output/alevin/quants_mat_cols.txt"/>
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211 <data name="quants_mat_rows_txt" label="${tool.name} on ${on_string}: row index (CB-ids)" format="txt" from_work_dir="output/alevin/quants_mat_rows.txt"/>
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212 <data name="quants_tier_mat" label="${tool.name} on ${on_string}: tier categorization" format="gz" from_work_dir="output/alevin/quants_tier_mat.gz"/>
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213 <data name="featureDump_txt" label="${tool.name} on ${on_string}: cell-level information (featureDump)" format="txt" from_work_dir="output/alevin/featureDump.txt"/>
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214 <data name="raw_cb_frequency_txt" label="${tool.name} on ${on_string}: raw CB classification frequencies" format="txt" from_work_dir="output/alevin/raw_cb_frequency.txt">
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215 <filter>output_files and 'dumpFeatures' in output_files</filter>
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216 </data>
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217 <data name="whitelist_txt" label="${tool.name} on ${on_string}: whitelist" format="txt" from_work_dir="output/alevin/whitelist.txt"/>
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218
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219 <data name="auxiliar_files" label="${tool.name} on ${on_string}: auxiliar info files" format="tgz" from_work_dir="aux_info.tar.gz">
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220 <filter>output_files and 'auxiliar_info' in output_files</filter>
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221 </data>
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222 <data name="salmon_quant_log" format="txt" label="${tool.name} on ${on_string}: Salmon log file" from_work_dir="output/logs/salmon_quant.log">
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223 <filter>output_files and 'salmon_log' in output_files</filter>
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224 </data>
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225 <data name="cmd_info" label="${tool.name} on ${on_string}: command info (JSON)" format="json" from_work_dir="output/cmd_info.json">
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226 <filter>output_files and 'commands' in output_files</filter>
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227 </data>
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228 <data name="flenDist_txt" format="txt" label="${tool.name} on ${on_string}: observed fragment length distribution" from_work_dir="output/libParams/flenDist.txt">
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229 <filter>output_files and 'fragment_length' in output_files</filter>
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230 </data>
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231 <data name="bfh_txt" label="${tool.name} on ${on_string}: full CB-EC-UMI-count data-structure" format="txt" from_work_dir="output/alevin/bfh.txt">
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232 <filter>output_files and 'dumpBfh' in output_files</filter>
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233 </data>
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234 <data name="quants_mean_mat" label="${tool.name} on ${on_string}: count matrix mean file" format="gz" from_work_dir="output/alevin/quants_mean_mat.gz">
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235 <filter>optional["numCellBootstraps"]</filter>
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236 </data>
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237 <data name="quants_var_mat" label="${tool.name} on ${on_string}: count matrix variance file" format="gz" from_work_dir="output/alevin/quants_var_mat.gz">
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238 <filter>optional["numCellBootstraps"]</filter>
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239 </data>
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240 <data name="quants_boot_rows_txt" label="${tool.name} on ${on_string}: bootstraps rows" format="txt" from_work_dir="output/alevin/quants_boot_rows.txt">
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241 <filter>optional["numCellBootstraps"]</filter>
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242 </data>
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243 <collection name="umigraphs" type="list" label="${tool.name} on ${on_string}: UMI graph PDFs">
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244 <filter>output_files and 'dumpUmiGraph' in output_files</filter>
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245 <discover_datasets pattern="(?P&lt;name&gt;.+)\.pdf" format="pdf" directory="fixed"/>
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246 </collection>
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247 </outputs>
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248 <tests>
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249 <test expect_num_outputs="8">
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250 <conditional name="refTranscriptSource">
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251 <param name="TranscriptSource" value="history"/>
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252 <section name="s_index">
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253 <param name="fasta" value="minitranscript.fa"/>
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254 </section>
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255 </conditional>
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256 <conditional name="pairstraight">
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257 <param name="readselect" value="paired"/>
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diff changeset
258 <param name="file1" value="fastqs/moreminifastq1.fastq.gz"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
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259 <param name="file2" value="fastqs/moreminifastq2.fastq.gz"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
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diff changeset
260 <param name="orientation" value="I"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
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diff changeset
261 <param name="strandedness" value="SR"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
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262 </conditional>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
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diff changeset
263 <conditional name="protocol_cond">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
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264 <param name="protocol" value="--chromium"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
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diff changeset
265 </conditional>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
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diff changeset
266 <param name="tgmap" value="minitxp.tsv"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
267 <param name="output_files" value="dumpFeatures"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
268 <section name="optional">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
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diff changeset
269 <param name="keepCBFraction" value="1"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
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diff changeset
270 <param name="freqThreshold" value="5"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
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diff changeset
271 <param name="dumpMtx" value="true"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
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diff changeset
272 </section>
14
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bgruening
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diff changeset
273 <output name="quants_mat_mtx" file="alevin_mat_01.mtx" compare="sim_size" ftype="mtx">
c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a
bgruening
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diff changeset
274 <assert_contents>
c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a
bgruening
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275 <has_text text="MatrixMarket" />
c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a
bgruening
parents: 11
diff changeset
276 <has_n_columns n="5" />
c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a
bgruening
parents: 11
diff changeset
277 <has_n_lines n="105" />
c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a
bgruening
parents: 11
diff changeset
278 </assert_contents>
c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a
bgruening
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279 </output>
11
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
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280 </test>
4
917f8e439160 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 5dfee8ad03865f59c3e1ac9dd5865fd40e4616ef"
bgruening
parents: 3
diff changeset
281 <test expect_num_outputs="11">
0
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
282 <conditional name="refTranscriptSource">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
283 <param name="TranscriptSource" value="history"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
284 <section name="s_index">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
285 <param name="fasta" value="minitranscript.fa"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
286 </section>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
287 </conditional>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
288 <conditional name="pairstraight">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
289 <param name="readselect" value="paired"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
290 <param name="file1" value="fastqs/moreminifastq1.fastq.gz"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
291 <param name="file2" value="fastqs/moreminifastq2.fastq.gz"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
292 <param name="orientation" value="I"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
293 <param name="strandedness" value="SR"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
294 </conditional>
11
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
295 <conditional name="protocol_cond">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
296 <param name="protocol" value="--chromium"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
297 </conditional>
0
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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diff changeset
298 <param name="tgmap" value="minitxp.tsv"/>
11
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
299 <param name="output_files" value="dumpFeatures"/>
8
04b494623f8e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 515548aaa4b79af78c6ffc6bd55f72ee9504d30f"
bgruening
parents: 7
diff changeset
300 <section name="optional">
04b494623f8e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 515548aaa4b79af78c6ffc6bd55f72ee9504d30f"
bgruening
parents: 7
diff changeset
301 <param name="keepCBFraction" value="1"/>
11
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
302 <param name="numCellBootstraps" value="2"/>
8
04b494623f8e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 515548aaa4b79af78c6ffc6bd55f72ee9504d30f"
bgruening
parents: 7
diff changeset
303 <param name="freqThreshold" value="5"/>
11
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
304 <param name="dumpMtx" value="true"/>
8
04b494623f8e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 515548aaa4b79af78c6ffc6bd55f72ee9504d30f"
bgruening
parents: 7
diff changeset
305 </section>
14
c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a
bgruening
parents: 11
diff changeset
306 <output name="quants_mat_mtx" file="alevin_mat_02.mtx" compare="sim_size" ftype="mtx" >
c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a
bgruening
parents: 11
diff changeset
307 <assert_contents>
c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a
bgruening
parents: 11
diff changeset
308 <has_text text="MatrixMarket" />
c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a
bgruening
parents: 11
diff changeset
309 <has_n_columns n="5" />
c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a
bgruening
parents: 11
diff changeset
310 <has_n_lines n="105" />
c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a
bgruening
parents: 11
diff changeset
311 </assert_contents>
c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a
bgruening
parents: 11
diff changeset
312 </output>
11
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
313 </test>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
314 <test expect_num_outputs="8">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
315 <conditional name="refTranscriptSource">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
316 <param name="TranscriptSource" value="history"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
317 <section name="s_index">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
318 <param name="fasta" value="minitranscript.fa"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
319 </section>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
320 </conditional>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
321 <conditional name="pairstraight">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
322 <param name="readselect" value="paired"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
323 <param name="file1" value="fastqs/moreminifastq1.fastq.gz"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
324 <param name="file2" value="fastqs/moreminifastq2.fastq.gz"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
325 <param name="orientation" value="I"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
326 <param name="strandedness" value="SR"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
327 </conditional>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
328 <conditional name="protocol_cond">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
329 <param name="protocol" value="-\-indropV2"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
330 <param name="w1" value="ATCAT"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
331 </conditional>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
332 <param name="tgmap" value="minitxp.tsv"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
333 <param name="output_files" value="dumpFeatures"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
334 <section name="optional">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
335 <param name="keepCBFraction" value="1"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
336 <param name="freqThreshold" value="5"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
337 <param name="dumpMtx" value="true"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents: 10
diff changeset
338 </section>
14
c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a
bgruening
parents: 11
diff changeset
339 <output name="quants_mat_mtx" file="alevin_mat_indropV2.mtx" compare="sim_size" ftype="mtx">
c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a
bgruening
parents: 11
diff changeset
340 <assert_contents>
c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a
bgruening
parents: 11
diff changeset
341 <has_text text="MatrixMarket" />
c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a
bgruening
parents: 11
diff changeset
342 <has_n_columns n="5" />
c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a
bgruening
parents: 11
diff changeset
343 <has_n_lines n="105" />
c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a
bgruening
parents: 11
diff changeset
344 </assert_contents>
c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a
bgruening
parents: 11
diff changeset
345 </output>
7
ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
bgruening
parents: 4
diff changeset
346 </test>
ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
bgruening
parents: 4
diff changeset
347 <test expect_num_outputs="14">
ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
bgruening
parents: 4
diff changeset
348 <conditional name="refTranscriptSource">
ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
bgruening
parents: 4
diff changeset
349 <param name="TranscriptSource" value="history"/>
ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
bgruening
parents: 4
diff changeset
350 <section name="s_index">
ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
bgruening
parents: 4
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351 <param name="fasta" value="minitranscript.fa"/>
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352 </section>
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353 </conditional>
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354 <conditional name="pairstraight">
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355 <param name="readselect" value="paired"/>
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356 <param name="file1" value="fastqs/moreminifastq1.fastq.gz"/>
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357 <param name="file2" value="fastqs/moreminifastq2.fastq.gz"/>
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358 <param name="orientation" value="I"/>
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359 <param name="strandedness" value="SR"/>
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360 </conditional>
11
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361 <conditional name="protocol_cond">
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362 <param name="protocol" value="--chromium"/>
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363 </conditional>
7
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364 <param name="tgmap" value="minitxp.tsv"/>
11
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365 <param name="output_files" value="dumpFeatures,salmon_log,fragment_length,auxiliar_info,dumpUmiGraph,dumpBfh,commands"/>
7
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366 <section name="optional">
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367 <param name="dumpMtx" value="true"/>
7
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368 </section>
14
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369 <output name="quants_mat_mtx" file="alevin_mat.mtx" compare="sim_size" ftype="mtx">
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370 <assert_contents>
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371 <has_text text="MatrixMarket" />
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372 <has_n_columns n="5" />
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373 <has_n_lines n="17" />
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374 </assert_contents>
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375 </output>
11
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376 <output name="salmon_quant_log" ftype="txt">
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377 <assert_contents>
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378 <has_text text="Index contained 322 targets"/>
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379 <has_text text="Counted 14 total reads in the equivalence classes"/>
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380 </assert_contents>
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381 </output>
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382 <output name="flenDist_txt" file="length_distribution.txt" ftype="txt"/>
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383 <output name="auxiliar_files" ftype="tgz">
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384 <assert_contents>
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385 <has_size value="1898" delta="100"/>
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386 </assert_contents>
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387 </output>
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388 <output_collection name="umigraphs" type="list" count="14">
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389 <element name="AGTGGGATCTTAACCT">
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390 <assert_contents>
14
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391 <has_size value="4661" delta="1000"/>
11
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392 </assert_contents>
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393 </element>
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394 </output_collection>
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395 <output name="bfh_txt" file="full_data_structure.txt" ftype="txt"/>
0
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396 </test>
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397 </tests>
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398 <help><![CDATA[
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399 @salmonhelp@
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400 @alevinhelp@
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401 ]]></help>
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402 <expand macro="citations"/>
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403 </tool>