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annotate sortmerna.xml @ 10:10b84b577117 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
author rnateam
date Sat, 21 Oct 2023 09:07:21 +0000
parents eb35257d2e29
children
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1 <tool id="bg_sortmerna" name="Filter with SortMeRNA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
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2 <description>of ribosomal RNAs in metatranscriptomic data</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
10
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6 <expand macro="requirements" />
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7 <stdio>
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8 <regex match="This program builds a Burst trie on an input rRNA database"
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9 source="both"
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10 level="fatal"
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11 description="Buildtrie program failed to execute." />
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12 <regex match="The database name"
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13 source="both"
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14 level="fatal"
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15 description="The database ${databases} has not been preprocessed using buildtrie before using SortMeRNA." />
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16 <regex match="ERROR"
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17 source="both"
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18 level="fatal"
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19 description="ERROR" />
0
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20 </stdio>
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21 <version_command>
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22 <![CDATA[
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23 sortmerna --version 2>&1|grep 'SortMeRNA version'
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24 ]]>
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25 </version_command>
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26 <command>
0
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27 <![CDATA[
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29 @PREPROCESSING@
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30
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31 mkdir -p './aligned' &&
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32 mkdir -p './kvdb_folder' &&
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33 mkdir -p './readb_folder' &&
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34 mkdir -p './idx_folder' &&
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35
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36 sortmerna
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37 #for $reference in $ref
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38 --ref '$reference'
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39 #end for
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40 -L '$databases_type.seed_length'
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41 --max_pos '$databases_type.max_pos'
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42 --aligned 'aligned'
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43 #if $sequencing_type.sequencing_type_selector == 'paired'
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44 --reads '$sequencing_type.forward_reads'
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45 --reads '$sequencing_type.reverse_reads'
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46 $sequencing_type.paired_type
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47 #elif $sequencing_type.sequencing_type_selector == 'interleaved'
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48 --reads '$sequencing_type.reads'
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49 --paired
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50 $sequencing_type.paired_type
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51 #else if $sequencing_type.sequencing_type_selector == 'paired_collection'
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52 --reads '${$sequencing_type.reads.forward}'
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53 --reads '${$sequencing_type.reads.reverse}'
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54 $sequencing_type.paired_type
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55 #else
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56 --reads '$sequencing_type.reads'
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57 #end if
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58 $strand_search
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59 $aligned_fastx.aligned_fastx_selector
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60 #if $aligned_fastx.aligned_fastx_selector == '--fastx'
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61 #if $aligned_fastx.other
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62 --other 'unaligned'
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63 #end if
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64 #end if
10
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65 #if $report.report_type == 'number_alignments'
8
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66 @ALIGNMENTS@
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67 @OTU_PICKING@
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68
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69 #if $report.report_num_alignments.output_alignments == 'all'
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70 --num_alignments '0'
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71 #else
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72 --num_alignments $report.report_num_alignments.num_alignments
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73 #end if
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74 $report.no_best
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75 #elif $report.report_type == 'min_lis'
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76 @ALIGNMENTS@
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77 @OTU_PICKING@
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78 --min_lis $report.min_lis
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79 #end if
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80 -e '$e_value'
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81 --match '$match'
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82 --mismatch '$mismatch'
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83 --gap_open '$gap_open'
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84 --gap_ext '$gap_ext'
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85 --threads \${GALAXY_SLOTS:-1}
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86 -m \${GALAXY_MEMORY_MB:-8192}
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87 --kvdb 'kvdb_folder'
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88 --idx-dir 'idx_folder'
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89 --readb 'readb_folder'
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90 #if $aligned_fastx.aligned_fastx_selector == '--fastx' and str($sequencing_type.sequencing_type_selector) == 'paired'
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91 --out2
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92 #end if
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93 #if $report.report_type != 'None'
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94 && samtools sort aligned.sam -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o '$output_bam'
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95 #end if
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96 && ls -lah
0
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97 ]]>
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98 </command>
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99 <inputs>
1
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100 <conditional name="sequencing_type">
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101 <param name="sequencing_type_selector" type="select" label="Sequencing type">
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102 <option value="not_paired">Single-end reads</option>
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103 <option value="paired">Paired-end reads</option>
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104 <option value="interleaved">Interleaved paired-end reads</option>
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105 <option value="paired_collection">Paired collection</option>
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106 </param>
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107 <when value="not_paired">
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108 <expand macro="reads_macro"/>
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109 </when>
1
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110 <when value="paired">
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111 <param name="forward_reads" type="data" format="fasta,fastq,fastq.gz,fasta.gz" label="Forward reads"/>
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112 <param name="reverse_reads" type="data" format="fasta,fastq,fastq.gz,fasta.gz" label="Reverse reads"/>
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113 <expand macro="paired_type_macro"/>
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114 </when>
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115 <when value="interleaved">
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116 <expand macro="reads_macro"/>
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117 <expand macro="paired_type_macro"/>
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118 </when>
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119 <when value="paired_collection">
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120 <param name="reads" format="fasta,fastq,fasta.gz,fastq.gz" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
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121 <expand macro="paired_type_macro"/>
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122 </when>
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123 </conditional>
2
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124 <param name="strand_search" type="select" label="Which strands to search">
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125 <option value="">Search both strands</option>
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126 <option value="-F">Search only the forward strand (-F)</option>
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127 <option value="-R">Search only the reverse-complementary strand (-R)</option>
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128 </param>
1
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129 <conditional name="databases_type">
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130 <param name="databases_selector" type="select" label="Databases to query"
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131 help="Public rRNA databases provided with SortMeRNA have been indexed. On the contrary, personal databases must be indexed each time SortMeRNA is launched. Please be patient, this may take some time depending on the size of the given database.">
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132 <option value="cached" selected="true">Public ribosomal databases</option>
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133 <option value="history">Databases from your history</option>
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134 </param>
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135 <when value="cached">
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136 <param name="input_databases" label="rRNA databases" type="select" optional="false" multiple="true">
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137 <options from_data_table="rRNA_databases">
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138 <column name="name" index="1"/>
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139 <column name="value" index="2"/>
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140 </options>
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141 <validator type="no_options" message="No options available. Contact your Galaxy administrator."/>
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142 </param>
8
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143 <expand macro="db_prep"/>
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144 </when>
1
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145 <when value="history">
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146 <param name="database_name" type="data" format="fasta,fasta.gz" multiple="true" label="rRNA databases" help="Your databases will be indexed first, which may take up to several minutes."/>
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147 <expand macro="db_prep"/>
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148 </when>
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149 </conditional>
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150 <!-- Outputs -->
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151 <conditional name="aligned_fastx">
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152 <param name="aligned_fastx_selector" type="select" label="Include aligned reads in FASTA/FASTQ format?">
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153 <option value="--fastx">Yes (--fastx)</option>
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154 <option value="">No</option>
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155 </param>
1
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156 <when value="--fastx">
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157 <param argument="--other" type="boolean" truevalue="True" falsevalue="False" label="Include rejected reads file?"/>
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158 </when>
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159 <when value=""/>
1
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160 </conditional>
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161 <conditional name="report">
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162 <param name="report_type" type="select" label="Alignment report">
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163 <option value="None">Do not report alignments</option>
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164 <option value="number_alignments">Report N number of alignments reaching E-value</option>
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165 <option value="min_lis">Report alignments that have the LIS of at least N seeds long reaching E-value</option>
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166 </param>
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167 <when value="None"/>
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168 <when value="number_alignments">
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169 <conditional name="report_num_alignments">
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170 <param argument="output_alignments" type="select" label="Number of output alignments" help="Report all alignments can be time consuming; this option is not suggested for high similarity rRNA databases.">
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171 <option value="all">All alignments reaching the E-value threshold are reported</option>
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172 <option value="custom">Custom number of alignments</option>
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173 </param>
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174 <when value="all" />
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175 <when value="custom">
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176 <param argument="--num_alignments" type="integer" min="1" max="100" value="1" label="Number of alignments to be reported"/>
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177 </when>
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178 </conditional>
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179 <param argument="--no-best" type="boolean" truevalue="--no-best" falsevalue="" checked="false" label="Disable best alignments search" help="The 'best' alignment is the highest
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180 scoring alignment out of All alignments of a read, and the read can potentially be aligned (reaching E-value threshold) to multiple reference sequences. By default the
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181 program searches for best alignments i.e. performs an exhaustive search over all references. Using '-no-best' will make the program to search just the first N alignments." />
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182 <expand macro="output_alignments"/>
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183 <expand macro="otu_picking"/>
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184 </when>
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185 <when value="min_lis">
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186 <param argument="--min_lis" type="integer" min="0" value="" label="Minimum Longest Increasing Subsequence (LIS)" help="It is computed using seeds, which are k-mers common to
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187 the read and the reference sequence. Sorted sequences of such seeds are used to filter the candidate references prior performing the Smith-Waterman alignment." />
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188 <expand macro="output_alignments"/>
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189 <expand macro="otu_picking"/>
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190 </when>
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191 </conditional>
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192 <param argument="--match" type="integer" min="0" max="10" value="2" label="SW score for a match"/>
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193 <param argument="--mismatch" type="integer" min="-10" max="0" value="-3" label="SW penalty for a mismatch"/>
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194 <param name="gap_open" type="integer" min="0" max="10" value="5" label="SW penalty for introducing a gap" help="(--gap_open)"/>
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195 <param name="gap_ext" type="integer" min="0" max="10" value="2" label="SW penalty for extending a gap" help="(--gap_ext)"/>
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196 <param name="e_value" argument="-e" type="float" min="0" max="10" value="1" label="E-value threshold" help="Defines the 'statistical significance' of a local alignment. Exponentially
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197 correllates with the Minimal Alignment score. Higher E-values (100, 1000, ...) cause more reads to pass the alignment threshold."/>
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198 <param argument="-N" type="boolean" truevalue="True" falsevalue="False" checked="false" label="SW penalty for ambiguous letters (N's)" help="Scored as --mismatch" />
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199 </inputs>
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200 <outputs>
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201 <data name="aligned" format_source="reads" from_work_dir="aligned.f*" label="${tool.name} on ${on_string}: Aligned reads">
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202 <filter>aligned_fastx['aligned_fastx_selector'] != ''</filter>
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203 <filter>sequencing_type['sequencing_type_selector'] != 'paired'</filter>
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204 </data>
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205 <data name="aligned_forward" format_source="forward_reads" from_work_dir="aligned_fwd*" label="${tool.name} on ${on_string}: Aligned forward reads">
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206 <filter>aligned_fastx['aligned_fastx_selector'] != '' and sequencing_type['sequencing_type_selector'] == 'paired'</filter>
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207 </data>
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208 <data name="aligned_reverse" format_source="reverse_reads" from_work_dir="aligned_rev*" label="${tool.name} on ${on_string}: Aligned reverse reads">
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209 <filter>aligned_fastx['aligned_fastx_selector'] != '' and sequencing_type['sequencing_type_selector'] == 'paired'</filter>
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210 </data>
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211 <data name="aligned_forward_singleton" format_source="forward_reads" from_work_dir="aligned_singleton_fwd*" label="${tool.name} on ${on_string}: Aligned forward singleton reads">
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212 <filter>aligned_fastx['aligned_fastx_selector'] != ''</filter>
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213 <filter>sequencing_type['sequencing_type_selector'] == 'paired'</filter>
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214 <filter>sequencing_type['paired_type'] == '--sout'</filter>
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215 </data>
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216 <data name="aligned_reverse_singleton" format_source="reverse_reads" from_work_dir="aligned_singleton_rev*" label="${tool.name} on ${on_string}: Aligned reverse singleton reads">
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217 <filter>aligned_fastx['aligned_fastx_selector'] != ''</filter>
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218 <filter>sequencing_type['sequencing_type_selector'] == 'paired'</filter>
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219 <filter>sequencing_type['paired_type'] == '--sout'</filter>
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220 </data>
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221 <data name="unaligned" format_source="reads" from_work_dir="aligned.f*" label="${tool.name} on ${on_string}: Unaligned reads">
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222 <filter>aligned_fastx['aligned_fastx_selector'] != ''</filter>
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223 <filter>aligned_fastx['other'] == True</filter>
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224 <filter>sequencing_type['sequencing_type_selector'] != 'paired'</filter>
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225 </data>
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226 <data name="unaligned_forward" format_source="forward_reads" from_work_dir="unaligned_fwd*" label="${tool.name} on ${on_string}: Unaligned forward reads">
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227 <filter>aligned_fastx['aligned_fastx_selector'] != ''</filter>
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228 <filter>aligned_fastx['other'] == True</filter>
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229 <filter>sequencing_type['sequencing_type_selector'] == 'paired'</filter>
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230 </data>
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231 <data name="unaligned_reverse" format_source="reverse_reads" from_work_dir="unaligned_rev*" label="${tool.name} on ${on_string}: Unaligned reverse reads">
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232 <filter>aligned_fastx['aligned_fastx_selector'] != ''</filter>
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233 <filter>aligned_fastx['other'] == True</filter>
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234 <filter>sequencing_type['sequencing_type_selector'] == 'paired'</filter>
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235 </data>
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236 <data name="unaligned_forward_singleton" format_source="forward_reads" from_work_dir="unaligned_fwd*" label="${tool.name} on ${on_string}: Unaligned forward singleton reads">
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237 <filter>aligned_fastx['aligned_fastx_selector'] != ''</filter>
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238 <filter>aligned_fastx['other'] == True</filter>
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239 <filter>sequencing_type['sequencing_type_selector'] == 'paired'</filter>
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240 <filter>sequencing_type['paired_type'] == '--sout'</filter>
8
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241 </data>
10
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242 <data name="unaligned_reverse_singleton" format_source="reverse_reads" from_work_dir="unaligned_rev*" label="${tool.name} on ${on_string}: Unaligned reverse singleton reads">
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243 <filter>aligned_fastx['aligned_fastx_selector'] != ''</filter>
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244 <filter>aligned_fastx['other'] == True</filter>
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245 <filter>sequencing_type['sequencing_type_selector'] == 'paired'</filter>
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246 <filter>sequencing_type['paired_type'] == '--sout'</filter>
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247 </data>
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248 <data name="output_bam" format="bam" label="${tool.name} on ${on_string}: Alignments (BAM)">
8
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249 <filter>report['report_type'] != 'None'</filter>
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250 </data>
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251 <data name="output_blast" format="tabular" from_work_dir="aligned.blast" label="${tool.name} on ${on_string}: BLAST report">
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252 <filter>report['report_type'] != 'None' and report['blast']['blast_output'] == 'True'</filter>
1
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253 <change_format>
3
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254 <when input="aligned_blast.aligned_blast_format" value="0" format="txt" />
1
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255 </change_format>
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256 </data>
10
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257 <data name="output_biom" format="txt" from_work_dir="aligned/otu_map.txt" label="${tool.name} on ${on_string}: OTU map">
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258 <filter>report['report_type'] != 'None' and report['otu']['otu_map'] == 'True'</filter>
8
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259 </data>
10
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260
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261 <data name="output_de_novo" format_source="reads" from_work_dir="aligned_denovo*" label="${tool.name} on ${on_string}: De novo reads matching database">
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262 <filter>report['report_type'] != 'None' and report['otu']['otu_map'] == 'True' and report['otu']['de_novo_otu'] == True</filter>
0
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263 </data>
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264 </outputs>
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265 <tests>
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266 <test expect_num_outputs="4">
8
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267 <conditional name="sequencing_type">
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268 <param name="sequencing_type_selector" value="not_paired" />
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269 <param name="reads" value="read_small.fastq" />
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270 </conditional>
0
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271 <param name="strand_search" value="" />
8
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272 <conditional name="databases_type">
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273 <param name="databases_selector" value="history" />
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274 <param name="database_name" value="ref_small.fasta" />
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275 </conditional>
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276 <conditional name="aligned_fastx">
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277 <param name="aligned_fastx_selector" value="--fastx" />
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278 <param name="other" value="True" />
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279 </conditional>
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280 <conditional name="report">
10
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281 <param name="report_type" value="number_alignments" />
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282 <conditional name="report_num_alignments">
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283 <param name="output_alignments" value="custom"/>
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284 <param name="num_alignments" value="1"/>
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285 </conditional>
8
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286 <conditional name="blast">
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287 <param name="blast_output" value="True"/>
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288 <param name="blast_format" value="1 cigar qcov"/>
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289 </conditional>
10
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290 </conditional>
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291 <param name="e_value" value="1"/>
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292 <param name="match" value="2"/>
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293 <param name="mismatch" value="-3" />
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294 <param name="gap_open" value="5"/>
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295 <param name="gap_ext" value="2"/>
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296 <param name="N" value="True"/>
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297 <output name="aligned" file="test1_aligned.fastq" />
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298 <output name="unaligned" file="test1_unaligned.fastq" />
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299 <output name="output_bam" file="test1_bam.bam" lines_diff="6" ftype="bam"/>
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300 <output name="output_blast" file="test1_blast.tabular"/>
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301 </test>
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302 <!-- test cached reference data -->
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303 <test expect_num_outputs="4">
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304 <conditional name="sequencing_type">
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305 <param name="sequencing_type_selector" value="not_paired" />
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306 <param name="reads" value="read_small.fastq" />
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307 </conditional>
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308 <param name="strand_search" value="" />
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309 <conditional name="databases_type">
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310 <param name="databases_selector" value="cached" />
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311 <param name="input_databases" value="ref_small" />
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312 </conditional>
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313 <conditional name="aligned_fastx">
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314 <param name="aligned_fastx_selector" value="--fastx" />
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315 <param name="other" value="True" />
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316 </conditional>
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317 <conditional name="report">
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318 <param name="report_type" value="number_alignments" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
319 <conditional name="report_num_alignments">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
320 <param name="output_alignments" value="custom"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
321 <param name="num_alignments" value="1"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
322 </conditional>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
323 <conditional name="blast">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
324 <param name="blast_output" value="True"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
325 <param name="blast_format" value="1 cigar qcov"/>
8
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
326 </conditional>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
327 </conditional>
3
59252ca85c74 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 5a8ffc52b7076d8d4fbc9649703bb4c0155b726c
rnateam
parents: 2
diff changeset
328 <param name="e_value" value="1"/>
59252ca85c74 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 5a8ffc52b7076d8d4fbc9649703bb4c0155b726c
rnateam
parents: 2
diff changeset
329 <param name="match" value="2"/>
59252ca85c74 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 5a8ffc52b7076d8d4fbc9649703bb4c0155b726c
rnateam
parents: 2
diff changeset
330 <param name="mismatch" value="-3" />
59252ca85c74 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 5a8ffc52b7076d8d4fbc9649703bb4c0155b726c
rnateam
parents: 2
diff changeset
331 <param name="gap_open" value="5"/>
59252ca85c74 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 5a8ffc52b7076d8d4fbc9649703bb4c0155b726c
rnateam
parents: 2
diff changeset
332 <param name="gap_ext" value="2"/>
10
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
333 <param name="N" value="True"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
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parents: 9
diff changeset
334 <output name="aligned" file="test1_aligned.fastq" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
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parents: 9
diff changeset
335 <output name="unaligned" file="test1_unaligned.fastq" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
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parents: 9
diff changeset
336 <output name="output_bam" file="test1_bam.bam" lines_diff="6" ftype="bam"/>
8
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
337 <output name="output_blast" file="test1_blast.tabular"/>
1
b482293b2987 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 844d980a7de5f199487ca9591420a23df63c5246-dirty
iuc
parents: 0
diff changeset
338 </test>
10
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
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parents: 9
diff changeset
339 <!-- testing 2 reference files from history .. apart from this same as previous test -->
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
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parents: 9
diff changeset
340 <test expect_num_outputs="4">
8
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
341 <conditional name="sequencing_type">
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
342 <param name="sequencing_type_selector" value="not_paired" />
10
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
343 <param name="reads" value="read_small.fastq" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
344 </conditional>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
345 <param name="strand_search" value="" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
346 <conditional name="databases_type">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
347 <param name="databases_selector" value="history" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
348 <param name="database_name" value="ref_small.fasta,ref_small_copy.fasta" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
349 </conditional>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
350 <conditional name="aligned_fastx">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
351 <param name="aligned_fastx_selector" value="--fastx" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
352 <param name="other" value="True" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
353 </conditional>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
354 <conditional name="report">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
355 <param name="report_type" value="number_alignments" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
356 <conditional name="report_num_alignments">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
357 <param name="output_alignments" value="custom"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
358 <param name="num_alignments" value="1"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
359 </conditional>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
360 <conditional name="blast">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
361 <param name="blast_output" value="True"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
362 <param name="blast_format" value="1 cigar qcov"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
363 </conditional>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
364 </conditional>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
365 <param name="e_value" value="1"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
366 <param name="match" value="2"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
367 <param name="mismatch" value="-3" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
368 <param name="gap_open" value="5"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
369 <param name="gap_ext" value="2"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
370 <param name="N" value="True"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
371 <output name="aligned" file="test1_aligned.fastq" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
372 <output name="unaligned" file="test1_unaligned.fastq" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
373 <output name="output_bam" file="test1_bam.bam" lines_diff="6" ftype="bam"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
374 <output name="output_blast" file="test1_blast.tabular"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
375 <assert_command>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
376 <has_text text="--ref" n="2"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
377 </assert_command>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
378 <assert_stdout>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
379 <has_text text="Processing reference [2] out of total [2] references"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
380 </assert_stdout>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
381 </test>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
382 <!-- testing 2 cached reference -->
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
383 <test expect_num_outputs="4">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
384 <conditional name="sequencing_type">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
385 <param name="sequencing_type_selector" value="not_paired" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
386 <param name="reads" value="read_small.fastq" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
387 </conditional>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
388 <param name="strand_search" value="" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
389 <conditional name="databases_type">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
390 <param name="databases_selector" value="cached" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
391 <param name="input_databases" value="ref_small,ref_small_copy" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
392 </conditional>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
393 <conditional name="aligned_fastx">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
394 <param name="aligned_fastx_selector" value="--fastx" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
395 <param name="other" value="True" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
396 </conditional>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
397 <conditional name="report">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
398 <param name="report_type" value="number_alignments" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
399 <conditional name="report_num_alignments">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
400 <param name="output_alignments" value="custom"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
401 <param name="num_alignments" value="1"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
402 </conditional>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
403 <conditional name="blast">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
404 <param name="blast_output" value="True"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
405 <param name="blast_format" value="1 cigar qcov"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
406 </conditional>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
407 </conditional>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
408 <param name="e_value" value="1"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
409 <param name="match" value="2"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
410 <param name="mismatch" value="-3" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
411 <param name="gap_open" value="5"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
412 <param name="gap_ext" value="2"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
413 <param name="N" value="True"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
414 <output name="aligned" file="test1_aligned.fastq" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
415 <output name="unaligned" file="test1_unaligned.fastq" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
416 <output name="output_bam" file="test1_bam.bam" lines_diff="6" ftype="bam"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
417 <output name="output_blast" file="test1_blast.tabular"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
418 <assert_command>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
419 <has_text text="--ref" n="2"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
420 </assert_command>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
421 <assert_stdout>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
422 <has_text text="Processing reference [2] out of total [2] references"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
423 </assert_stdout>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
424 </test>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
425 <test expect_num_outputs="1">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
426 <conditional name="sequencing_type">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
427 <param name="sequencing_type_selector" value="not_paired" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
428 <param name="reads" value="read_small.fastq" />
8
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
429 </conditional>
1
b482293b2987 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 844d980a7de5f199487ca9591420a23df63c5246-dirty
iuc
parents: 0
diff changeset
430 <param name="strand_search" value="" />
8
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
431 <conditional name="databases_type">
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
432 <param name="databases_selector" value="history" />
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
433 <param name="database_name" value="ref_small.fasta" />
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
434 </conditional>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
435 <conditional name="aligned_fastx">
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
436 <param name="aligned_fastx_selector" value="--fastx" />
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
437 <param name="other" value="False" />
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
438 </conditional>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
439 <conditional name="report">
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
440 <param name="report_type" value="None" />
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
441 </conditional>
3
59252ca85c74 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 5a8ffc52b7076d8d4fbc9649703bb4c0155b726c
rnateam
parents: 2
diff changeset
442 <param name="e_value" value="1"/>
59252ca85c74 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 5a8ffc52b7076d8d4fbc9649703bb4c0155b726c
rnateam
parents: 2
diff changeset
443 <param name="match" value="2"/>
59252ca85c74 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 5a8ffc52b7076d8d4fbc9649703bb4c0155b726c
rnateam
parents: 2
diff changeset
444 <param name="mismatch" value="-3" />
59252ca85c74 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 5a8ffc52b7076d8d4fbc9649703bb4c0155b726c
rnateam
parents: 2
diff changeset
445 <param name="gap_open" value="5"/>
59252ca85c74 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 5a8ffc52b7076d8d4fbc9649703bb4c0155b726c
rnateam
parents: 2
diff changeset
446 <param name="gap_ext" value="2"/>
10
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
447 <param name="N" value="True"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
448 <output name="aligned" file="test2_aligned.fasta" />
8
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
449 </test>
10
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
450 <test expect_num_outputs="5">
8
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
451 <conditional name="sequencing_type">
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
452 <param name="sequencing_type_selector" value="paired" />
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
453 <param name="forward_reads" value="forward_reads.fastq" />
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
454 <param name="reverse_reads" value="reverse_reads.fastq" />
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
455 <param name="paired_type" value="--paired_in"/>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
456 </conditional>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
457 <param name="strand_search" value="" />
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
458 <conditional name="databases_type">
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
459 <param name="databases_selector" value="history" />
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
460 <param name="database_name" value="ref_small.fasta" />
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
461 <param name="seed_length" value="18" />
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
462 <param name="max_pos" value="100000"/>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
463 </conditional>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
464 <conditional name="aligned_fastx">
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
465 <param name="aligned_fastx_selector" value="--fastx" />
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
466 <param name="other" value="True" />
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
467 </conditional>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
468 <conditional name="report">
10
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
469 <param name="report_type" value="number_alignments" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
470 <conditional name="report_num_alignments">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
471 <param name="output_alignments" value="all"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
472 </conditional>
8
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
473 <param name="print_all_reads" value="False" />
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
474 <conditional name="blast">
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
475 <param name="blast_output" value="False"/>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
476 </conditional>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
477 <conditional name="otu">
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
478 <param name="otu_map" value="False"/>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
479 </conditional>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
480 </conditional>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
481 <param name="e_value" value="1"/>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
482 <param name="match" value="2"/>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
483 <param name="mismatch" value="-3" />
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
484 <param name="gap_open" value="5"/>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
485 <param name="gap_ext" value="2"/>
10
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
486 <param name="N" value="True"/>
8
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
487 <output name="aligned_forward" file="test3_aligned_forward.fastq" />
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
488 <output name="aligned_reverse" file="test3_aligned_reverse.fastq" />
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
489 <output name="unaligned_forward" file="test3_unaligned_forward.fastq" />
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
490 <output name="unaligned_reverse" file="test3_unaligned_reverse.fastq" />
10
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
491 <output name="output_bam" file="test3_bam.bam" lines_diff="6" ftype="bam"/>
8
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
492 </test>
10
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
493 <test expect_num_outputs="3">
8
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
494 <conditional name="sequencing_type">
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
495 <param name="sequencing_type_selector" value="not_paired" />
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
496 <param name="reads" value="test4_input.fasta" />
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
497 </conditional>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
498 <param name="strand_search" value="" />
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
499 <conditional name="databases_type">
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
500 <param name="databases_selector" value="history" />
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
501 <param name="database_name" value="ref_small.fasta" />
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
502 <param name="seed_length" value="18" />
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
503 <param name="max_pos" value="100000"/>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
504 </conditional>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
505 <conditional name="aligned_fastx">
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
506 <param name="aligned_fastx_selector" value="" />
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
507 </conditional>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
508 <conditional name="report">
10
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
509 <param name="report_type" value="number_alignments" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
510 <conditional name="report_num_alignments">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
511 <param name="output_alignments" value="all"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
512 </conditional>
8
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
513 <param name="print_all_reads" value="False" />
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
514 <conditional name="blast">
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
515 <param name="blast_output" value="False"/>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
516 </conditional>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
517 <conditional name="otu">
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
518 <param name="otu_map" value="True"/>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
519 <param name="id" value="0.97"/>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
520 <param name="coverage" value="0.97" />
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
521 <param name="de_novo_otu" value="True"/>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
522 </conditional>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
523 </conditional>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
524 <param name="e_value" value="1"/>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
525 <param name="match" value="2"/>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
526 <param name="mismatch" value="-3" />
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
527 <param name="gap_open" value="5"/>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
528 <param name="gap_ext" value="2"/>
10
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
529 <param name="N" value="True"/>
8
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
530 <output name="output_bam" file="test4_bam.bam" compare="sim_size" delta="200" />
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
531 <output name="output_biom" file="test4_biom.txt"/>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
rnateam
parents: 7
diff changeset
532 <output name="output_de_novo" file="test4_de_novo.fasta"/>
0
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
rnateam
parents:
diff changeset
533 </test>
10
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
534 <test expect_num_outputs="5">
9
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
535 <conditional name="sequencing_type">
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
536 <param name="sequencing_type_selector" value="paired" />
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
537 <param name="forward_reads" value="forward_reads.fasta" />
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
538 <param name="reverse_reads" value="reverse_reads.fasta" />
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
539 <param name="paired_type" value=""/>
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
540 </conditional>
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
541 <param name="strand_search" value="" />
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
542 <conditional name="databases_type">
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
543 <param name="databases_selector" value="history" />
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
544 <param name="database_name" value="ref_small.fasta" />
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
545 <param name="seed_length" value="18" />
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
546 <param name="max_pos" value="100000"/>
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
547 </conditional>
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
548 <conditional name="aligned_fastx">
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
549 <param name="aligned_fastx_selector" value="--fastx" />
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
550 <param name="other" value="True" />
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
551 </conditional>
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
552 <conditional name="report">
10
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
553 <param name="report_type" value="number_alignments" />
9
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
554 <param name="print_all_reads" value="False" />
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
555 <conditional name="blast">
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
556 <param name="blast_output" value="False"/>
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
557 </conditional>
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
558 <conditional name="otu">
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
559 <param name="otu_map" value="False"/>
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
560 </conditional>
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
561 </conditional>
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
562 <param name="e_value" value="1"/>
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
563 <param name="match" value="2"/>
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
564 <param name="mismatch" value="-3" />
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
565 <param name="gap_open" value="5"/>
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
566 <param name="gap_ext" value="2"/>
10
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
567 <param name="N" value="True"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
568 <output name="aligned_forward" file="test5_aligned_forward.fasta" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
569 <output name="aligned_reverse" file="test5_aligned_reverse.fasta" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
570 <output name="output_bam" file="test5_bam.bam" lines_diff="6" ftype="bam"/>
9
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
571 </test>
10
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
572 <test expect_num_outputs="5">
9
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
573 <conditional name="sequencing_type">
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
574 <param name="sequencing_type_selector" value="paired" />
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
575 <param name="forward_reads" value="forward_reads.fasta" />
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
576 <param name="reverse_reads" value="reverse_reads.fasta" />
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
577 <param name="paired_type" value="--paired_out"/>
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
578 </conditional>
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
579 <param name="strand_search" value="" />
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
580 <conditional name="databases_type">
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
581 <param name="databases_selector" value="history" />
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
582 <param name="database_name" value="ref_small.fasta" />
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
583 <param name="seed_length" value="18" />
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
584 <param name="max_pos" value="100000"/>
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
585 </conditional>
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
586 <conditional name="aligned_fastx">
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
587 <param name="aligned_fastx_selector" value="--fastx" />
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
588 <param name="other" value="True" />
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
589 </conditional>
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
590 <conditional name="report">
10
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
591 <param name="report_type" value="number_alignments" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
592 <conditional name="report_num_alignments">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
593 <param name="output_alignments" value="all"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
594 </conditional>
9
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
595 <param name="print_all_reads" value="False" />
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
596 <conditional name="blast">
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
597 <param name="blast_output" value="False"/>
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
598 </conditional>
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
599 <conditional name="otu">
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
600 <param name="otu_map" value="False"/>
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
601 </conditional>
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
602 </conditional>
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
603 <param name="e_value" value="1"/>
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
604 <param name="match" value="2"/>
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
605 <param name="mismatch" value="-3" />
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
606 <param name="gap_open" value="5"/>
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
607 <param name="gap_ext" value="2"/>
10
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
608 <param name="N" value="True"/>
9
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
609 <output name="aligned_forward" file="test6_aligned_forward.fasta" />
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
610 <output name="aligned_reverse" file="test6_aligned_reverse.fasta" />
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
611 <output name="unaligned_forward" file="test6_unaligned_forward.fasta" />
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
rnateam
parents: 8
diff changeset
612 <output name="unaligned_reverse" file="test6_unaligned_reverse.fasta" />
10
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
613 <output name="output_bam" file="test6_bam.bam" lines_diff="6" ftype="bam"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
614 </test>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
615 <test expect_num_outputs="1">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
616 <conditional name="sequencing_type">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
617 <param name="sequencing_type_selector" value="paired" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
618 <param name="forward_reads" value="forward_reads.fasta" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
619 <param name="reverse_reads" value="reverse_reads.fasta" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
620 </conditional>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
621 <conditional name="databases_type">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
622 <param name="databases_selector" value="history" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
623 <param name="database_name" value="ref_small.fasta" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
624 </conditional>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
625 <conditional name="aligned_fastx">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
626 <param name="aligned_fastx_selector" value="" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
627 </conditional>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
628 <conditional name="report">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
629 <param name="report_type" value="min_lis" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
630 <param name="min_lis" value="1"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
631 </conditional>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
632 <output name="output_bam" file="test7_bam.bam" lines_diff="6" ftype="bam"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
633 </test>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
634 <test expect_num_outputs="9">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
635 <conditional name="sequencing_type">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
636 <param name="sequencing_type_selector" value="paired" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
637 <param name="forward_reads" value="forward_reads.fastq" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
638 <param name="reverse_reads" value="reverse_reads.fastq" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
639 <param name="paired_type" value="--sout"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
640 </conditional>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
641 <param name="strand_search" value="" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
642 <conditional name="databases_type">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
643 <param name="databases_selector" value="history" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
644 <param name="database_name" value="ref_small.fasta" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
645 <param name="seed_length" value="18" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
646 <param name="max_pos" value="100000"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
647 </conditional>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
648 <conditional name="aligned_fastx">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
649 <param name="aligned_fastx_selector" value="--fastx" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
650 <param name="other" value="True" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
651 </conditional>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
652 <conditional name="report">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
653 <param name="report_type" value="number_alignments" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
654 <conditional name="report_num_alignments">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
655 <param name="output_alignments" value="all"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
656 </conditional>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
657 <param name="print_all_reads" value="False" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
658 <conditional name="blast">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
659 <param name="blast_output" value="False"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
660 </conditional>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
661 <conditional name="otu">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
662 <param name="otu_map" value="False"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
663 </conditional>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
664 </conditional>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
665 <param name="e_value" value="1"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
666 <param name="match" value="2"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
667 <param name="mismatch" value="-3" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
668 <param name="gap_open" value="5"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
669 <param name="gap_ext" value="2"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
670 <param name="N" value="True"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
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parents: 9
diff changeset
671 <output name="aligned_forward_singleton" file="test8_aligned_forward_singleton.fastq" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
672 <output name="aligned_reverse_singleton" file="test8_aligned_reverse_singleton.fastq" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
673 <output name="output_bam" file="test8_bam.bam" lines_diff="6" ftype="bam"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
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parents: 9
diff changeset
674 </test>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
675 <test expect_num_outputs="1">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
676 <conditional name="sequencing_type">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
677 <param name="sequencing_type_selector" value="interleaved" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
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parents: 9
diff changeset
678 <param name="reads" value="interlaced_reads.fastq.gz" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
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parents: 9
diff changeset
679 </conditional>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
680 <conditional name="databases_type">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
681 <param name="databases_selector" value="history" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
682 <param name="database_name" value="ref_small.fasta" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
683 </conditional>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
684 <output name="aligned" file="test9_aligned.fastq.gz" compare="sim_size"/>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
685 </test>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
686 <test expect_num_outputs="1">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
687 <conditional name="sequencing_type">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
688 <param name="sequencing_type_selector" value="paired_collection" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
689 <param name="reads">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
690 <collection type="paired">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
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parents: 9
diff changeset
691 <element name="forward" value="forward_reads.fastq" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
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diff changeset
692 <element name="reverse" value="reverse_reads.fastq" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
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parents: 9
diff changeset
693 </collection>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
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parents: 9
diff changeset
694 </param>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
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parents: 9
diff changeset
695 </conditional>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
696 <conditional name="databases_type">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
rnateam
parents: 9
diff changeset
697 <param name="databases_selector" value="history" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
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parents: 9
diff changeset
698 <param name="database_name" value="ref_small.fasta" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
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diff changeset
699 </conditional>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
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parents: 9
diff changeset
700 <conditional name="aligned_fastx">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
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parents: 9
diff changeset
701 <param name="aligned_fastx_selector" value="" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
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diff changeset
702 </conditional>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
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parents: 9
diff changeset
703 <conditional name="report">
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
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parents: 9
diff changeset
704 <param name="report_type" value="number_alignments" />
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
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705 </conditional>
10b84b577117 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
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diff changeset
706 <output name="output_bam" file="test10_bam.bam" lines_diff="8" ftype="bam"/>
9
eb35257d2e29 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
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parents: 8
diff changeset
707 </test>
0
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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diff changeset
708 </tests>
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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diff changeset
709 <help>
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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diff changeset
710 <![CDATA[
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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diff changeset
711 **What it does**
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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diff changeset
712
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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diff changeset
713 SortMeRNA_ is a software designed to rapidly filter ribosomal RNA fragments
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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diff changeset
714 from metatransriptomic data produced by next-generation sequencers.
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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715 It is capable of handling large RNA databases and sorting out all fragments
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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716 matching to the database with high accuracy and specificity.
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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diff changeset
717
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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diff changeset
718 .. _SortMeRNA: http://bioinfo.lifl.fr/RNA/sortmerna/
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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diff changeset
719
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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diff changeset
720
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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diff changeset
721 **Input**
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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diff changeset
722
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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diff changeset
723 The input is one file of reads in FASTA or FASTQ format and any number of rRNA databases to search against.
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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diff changeset
724 If the user has two foward-reverse paired-sequencing reads files, they may use
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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diff changeset
725 the script "merge_paired_reads.sh" to interleave the reads into one file, preserving their order.
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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parents:
diff changeset
726
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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diff changeset
727 If the sequencing type for the reads is paired-ended, the user has two options under
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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728 "Sequencing type" to filter the reads and preserve their order in the file.
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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729 For a further example of each option, please refer to Section 4.2.3 in the `SortMeRNA User Manual`_.
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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diff changeset
730
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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diff changeset
731 .. _sortmerna user manual: http://bioinfo.lifl.fr/RNA/sortmerna/code/SortMeRNA-user-manual-v1.7.pdf
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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diff changeset
732
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733
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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734 **Output**
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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735
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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736 The output will follow the same format (FASTA or FASTQ) as the reads. Optionally, a statistic file for the rRNA content of reads, as well as rRNA subunit distribution can be generated.
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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737
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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738
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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739 **rRNA databases**
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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740
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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741 SortMeRNA is distributed with 8 representative rRNA databases, which were
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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742 all constructed from the SILVA SSU,LSU (version 111) and the RFAM 5/5.8S
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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743 (version 11.0) databases using the tool UCLUST.
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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744
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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745 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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746 | Representative database | id % | average id% | # seq (clustered) | Origin | # seq (original) |
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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747 +==========================+======+=============+===================+========================+===================+
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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748 | SILVA 16S bacteria | 85 | 91.6 | 8174 | SILVA SSU Ref NR v.111 | 244077 |
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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749 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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750 | SILVA 16S archaea | 95 | 96.7 | 3845 | SILVA SSU Ref NR v.111 | 10919 |
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751 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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752 | SILVA 18S eukarya | 95 | 96.7 | 4512 | SILVA SSU Ref NR v.111 | 31862 |
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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753 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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754 | SILVA 23S bacteria | 98 | 99.4 | 3055 | SILVA LSU Ref v.111 | 19580 |
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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755 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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756 | SILVA 23s archaea | 98 | 99.5 | 164 | SILVA LSU Ref v.111 | 405 |
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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757 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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758 | SILVA 28S eukarya | 98 | 99.1 | 4578 | SILVA LSU Ref v.111 | 9321 |
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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759 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
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760 | Rfam 5S archaea/bacteria | 98 | 99.2 | 59513 | RFAM | 116760 |
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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761 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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762 | Rfam 5.8S eukarya | 98 | 98.9 | 13034 | RFAM | 225185 |
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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763 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
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764
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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765 id %: members of the cluster must have identity at least 'id %' identity with the representative sequence
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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766
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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767 average id %: average identity of a cluster member to the representative sequence
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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768
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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769 The user may also choose to use their own rRNA databases.
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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770
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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771 .. class:: warningmark
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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772
2
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773 Note that your personal databases are indexed each time. The public ribosomal
3699b6b771e0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707
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774 databases are indexed when added, but they can be re-indexed with non-default indexing
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775 parameters. The indexing may take some time depending on the size of the given database.
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776
0
a8ac09e937f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 04cfb5475292e4fd1f7c0ca86d8d0d5e5f886c3d-dirty
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777 ]]>
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778 </help>
10
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779 <expand macro="citations" />
0
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780 </tool>