Mercurial > repos > bgruening > diamond

annotate diamond.xml @ 8:54f751e413f4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
author iuc
date Mon, 22 Mar 2021 13:21:23 +0000
parents 62c9df8382c2
children f921014aba5a
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62c9df8382c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
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1 <tool id="bg_diamond" name="Diamond" version="@VERSION@.0" profile="19.01">
0
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2 <description>alignment tool for short sequences against a protein database</description>
1
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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7 <expand macro="stdio" />
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8 <expand macro="version_command" />
8
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
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9 <command detect_errors="aggressive">
0
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10 <![CDATA[
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11
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12 #if $ref_db_source.db_source == "history":
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13 ln -s $ref_db_source.reference_database ./database.dmnd
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14 #else:
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15 ln -s ${ref_db_source.index.fields.db_path} ./database.dmnd
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16 #end if
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17
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18 &&
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19
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20 diamond
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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21 $method_cond.method_select
8
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
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22 --quiet
0
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23 --threads "\${GALAXY_SLOTS:-12}"
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24 --db ./database
1
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25 --query '$query'
6
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26 #if $method_cond.method_select == "blastx"
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27 --query-gencode '$method_cond.query_gencode'
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28 --strand '$method_cond.query_strand'
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54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
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29 --min-orf $method_cond.min_orf
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
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30 #if $method_cond.frameshift_cond.frameshift_select == 'yes'
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
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31 --frameshift $method_cond.frameshift_cond.frameshift
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
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32 $method_cond.frameshift_cond.range_culling
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33 #end if
8
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
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34 #else if $method_cond.method_select == "blastp"
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
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35 $method_cond.no_self_hits
3
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36 #end if
1
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37
6
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38 @OUTPUT_ARGS@
1
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39
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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40 --compress '0'
8
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
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41 $sens_cond.sensitivity
3
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42
6
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43 #if str($gapopen) != "":
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44 --gapopen '$gapopen'
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45 #end if
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46 #if str($gapextend) != "":
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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47 --gapextend '$gapextend'
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48 #end if
1
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49 --matrix '$matrix'
8
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
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50 --comp-based-stats '$method_cond.comp_based_stats'
6
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51 --masking '$masking'
0
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52
6
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53 @HITFILTER_ARGS@
0
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54
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55 #if str($filter_score.filter_score_select) == 'evalue':
1
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56 --evalue '$filter_score.evalue'
0
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57 #else:
1
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58 --min-score '$filter_score.min_score'
0
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59 #end if
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60
1
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61 --id '$id'
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62 --query-cover '$query_cover'
6
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63 --subject-cover '$subject_cover'
8
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64 --block-size '$sens_cond.block_size'
6
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65 #if str($unal) == '1':
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66 --unal 1 --un '$unalqueries'
6
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67 #end if
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68 #if $tax_cond.tax_select == 'file':
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69 --taxonlist `cat '$tax_cond.taxonlistfile' | grep -v "^#" | grep -v "^$" | tr "\n" "," | sed 's/,$//'`
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70 #else if $tax_cond.tax_select == 'list':
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71 --taxonlist '$tax_cond.taxonlist'
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72 #end if
0
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73 ]]>
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74 </command>
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75 <inputs>
6
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76 <conditional name="method_cond">
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77 <param name="method_select" type="select" label="What do you want to align?" help="(blastp/blastx)">
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78 <option value="blastp">Align amino acid query sequences (blastp)</option>
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79 <option value="blastx">Align DNA query sequences (blastx)</option>
3
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80 </param>
6
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81 <when value="blastx">
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82 <param name="query_gencode" argument="--query-gencode" type="select" label="Genetic code used for translation of query in BLASTX mode" help="">
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83 <option value="1">The Standard Code</option>
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84 <option value="2">The Vertebrate Mitochondrial Code</option>
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85 <option value="3">The Yeast Mitochondrial Code</option>
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86 <option value="4">The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
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87 <option value="5">The Invertebrate Mitochondrial Code</option>
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88 <option value="6">The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
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89 <option value="9">The Echinoderm and Flatworm Mitochondrial Code</option>
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90 <option value="10">The Euplotid Nuclear Code</option>
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91 <option value="11">The Bacterial, Archaeal and Plant Plastid Code</option>
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92 <option value="12">The Alternative Yeast Nuclear Code</option>
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93 <option value="13">The Ascidian Mitochondrial Code</option>
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bgruening
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94 <option value="14">The Alternative Flatworm Mitochondrial Code</option>
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95 <option value="16">Chlorophycean Mitochondrial Code</option>
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96 <option value="21">Trematode Mitochondrial Code</option>
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97 <option value="22">Scenedesmus obliquus Mitochondrial Code</option>
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98 <option value="23">Thraustochytrium Mitochondrial Code</option>
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99 <option value="24">Pterobranchia Mitochondrial Code</option>
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100 <option value="25">Candidate Division SR1 and Gracilibacteria Code</option>
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101 <option value="26">Pachysolen tannophilus Nuclear Code</option>
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102 </param>
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103 <param argument="--min-orf" name="min_orf" type="integer" value="1" label="ignore translated sequences without an open reading frame of at least this length" help="By default this feature is disabled for sequences of length below 30, set to 20 for sequences of length below 100, and set to 40 otherwise. Setting this option to 1 will disable this feature" />
7
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104
6
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105 <param name="query_strand" argument="--strand" type="select" label="query strands to search" help="">
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106 <option value="both" selected="True">Both</option>
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107 <option value="plus">Plus</option>
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108 <option value="minus">Minus</option>
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109 </param>
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110 <conditional name="frameshift_cond">
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111 <param name="frameshift_select" type="select" label="Allow for frameshifts?" help="">
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112 <option value="yes">yes</option>
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113 <option value="no" selected="true">no</option>
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114 </param>
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115 <when value="yes">
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116 <param argument="--range-culling" name="range_culling" type="boolean" truevalue="--range-culling" falsevalue="" checked="false" label="restrict hit culling to overlapping query ranges" help="This feature is designed for long query DNA sequences that may span several genes. In these cases, the default of reporting the 25 best overall hits could cause hits to a lower scoring gene to be overshadowed. But just increasing the number of alignments reported will bloat the output size and reduce performance. Using this feature along with -k 25 (default), a hit will only be deleted if at least 50% of its query range is spanned by at least 25 higher or equal scoring hits. Using this feature along with --top 10, a hit will only be deleted if its score is more than 10% lower than that of a higher scoring hit over at least 50% of its query range. The percentage is configurable using --range-cover. Note that this feature is currently only available in frameshift alignment mode"/>
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117 <param argument="--frameshift" type="integer" value="0" label="frame shift penalty" help="Values around 15 are reasonable for this parameter. Enabling this feature will have the aligner tolerate missing bases in DNA sequences and is most recommended for long, error-prone sequences like MinION reads. In the pairwise output format, frameshifts will be indicated by \ and / for a shift by +1 and -1 nucleotide in the direction of translation respectively." />
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118 </when>
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119 <when value="no"/>
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120 </conditional>
8
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121
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122 <param name="comp_based_stats" argument="--comp-based-stats" type="select" label="Composition based statistics" help="Compositionally biased sequences often cause false positive matches, which are effectively filtered by this algorithm in a way similar to the composition based statistics used by BLAST">
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123 <option value="0">Disable</option>
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124 <option value="1" selected="True">Default mode (Hauser, 2016)</option>
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125 </param>
6
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126 </when>
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127 <when value="blastp">
8
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128 <param name="no_self_hits" argument="--no-self-hits" type="boolean" truevalue="--no-self-hits" falsevalue="" checked="true" label="suppress reporting of identical self hits?" help=""/>
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129
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130 <param name="comp_based_stats" argument="--comp-based-stats" type="select" label="Composition based statistics" help="Compositionally biased sequences often cause false positive matches, which are effectively filtered by this algorithm in a way similar to the composition based statistics used by BLAST">
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131 <option value="0">Disable</option>
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132 <option value="1" selected="True">Default mode (Hauser, 2016)</option>
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133 <option value="2">Compositional matrix adjust conditioned on sequence properties, simplified (Yu, 2005)</option>
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134 <option value="3">Compositional matrix adjust conditioned on sequence properties (Yu, 2005)</option>
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135 <option value="4">Compositional matrix adjust unconditionally (Yu, 2005)</option>
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136 </param>
6
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137 </when>
3
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138 </conditional>
1
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139 <param argument="--query" type="data" format="fasta,fastq" label="Input query file in FASTA or FASTQ format" />
0
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140 <conditional name="ref_db_source">
6
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141 <param name="db_source" type="select" label="Will you select a reference database from your history or use a built-in index?" help="Built-ins were indexed using default options">
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142 <option value="indexed">Use a built-in index</option>
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143 <option value="history">Use one from the history</option>
0
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144 </param>
6
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145 <when value="indexed">
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146 <param name="index" type="select" label="Select a reference database" help="If your database of interest is not listed, contact your Galaxy admin">
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147 <options from_data_table="diamond_database">
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148 <filter type="sort_by" column="2"/>
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149 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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150 </options>
1
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151 </param>
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152 </when>
6
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153 <when value="history">
8
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154 <param name="reference_database" argument="--db" type="data" format="dmnd" label="Select the reference database" />
0
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155 </when>
98037ef3d2a9 Imported from capsule None
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156 </conditional>
8
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157 <expand macro="output_type_macro">
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158 <!-- Taxonomy features are not supported for the DAA format (i.e.
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159 can't be used in diamond view) -->
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160 <option value="staxids">unique Subject Taxonomy ID(s), separated by a ';' (in numerical order)</option>
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161 <option value="sskingdoms">Subject super kingdoms</option>
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162 <option value="skingdoms">Subject kingdoms</option>
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163 <option value="sphylums">Subject phylums</option>
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164 </expand>
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165 <conditional name="sens_cond">
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166 <param name='sensitivity' type="select" label="Sensitivity Mode" help="Choose one of the sensitivity modes. The default mode is mainly designed for short read alignment, i.e. finding significant matches of >50 bits on 30-40aa fragments. The sensitive mode is a lot more sensitive than the default and generally recommended for aligning longer sequences. The more sensitive mode provides even more sensitivity. More sensitivity may increase computation time.">
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167 <option value="" selected="True">Default</option>
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168 <option value="--mid-sensitive">Mid Sensitive (--mid-sensitive)</option>
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169 <option value="--sensitive">Sensitive (--sensitive)</option>
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170 <option value="--more-sensitive">More Sensitive (--more-sensitive)</option>
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171 <option value="--very-sensitive">Very Sensitive (--very-sensitive)</option>
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172 <option value="--ultra-sensitive">Ultra Sensitive (--ultra-sensitive)</option>
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173 </param>
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174 <when value="">
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175 <expand macro="block_size_low_sens"/>
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176 </when>
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177 <when value="--mid-sensitive">
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178 <expand macro="block_size_low_sens"/>
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179 </when>
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180 <when value="--sensitive">
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181 <expand macro="block_size_low_sens"/>
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182 </when>
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183 <when value="--more-sensitive">
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184 <expand macro="block_size_low_sens"/>
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185 </when>
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186 <when value="--very-sensitive">
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parents: 7
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187 <expand macro="block_size_hi_sens"/>
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parents: 7
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188 </when>
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parents: 7
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189 <when value="--ultra-sensitive">
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190 <expand macro="block_size_hi_sens"/>
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parents: 7
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191 </when>
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192 </conditional>
6
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193 <param argument="--matrix" type="select" label="Scoring matrix" help="In parentheses are the supported values for (gap open)/(gap extend). In brackets are default gap penalties">
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194 <option value="BLOSUM45">BLOSUM45 ((10-13)/3; (12-16)/2; (16-19)/1) [14/2]</option>
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195 <option value="BLOSUM50">BLOSUM50 ((9-13)/3; (12-16)/2; (15-19)/1) [13/2]</option>
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196 <option value="BLOSUM62" selected="True">BLOSUM62 ((6-11)/2; (9-13)/1) [11/1]</option>
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197 <option value="BLOSUM80">BLOSUM80 ((6-9)/2; 13/2; 25/2; (9-11)/1) [10/1]</option>
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198 <option value="BLOSUM90">BLOSUM90 ((6-9)/2; (9-11)/1) [10/1]</option>
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199 <option value="PAM250">PAM250 ((11-15)/3; (13-17)/2; (17-21)/1) [14/2]</option>
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200 <option value="PAM70">PAM70 ((6-8)/2; (9-11)/1) [10/1]</option>
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201 <option value="PAM30">PAM30 ((5-7)/2; (8-10)/1) [9/1]</option>
3
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parents: 1
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202 </param>
6
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203 <param argument="--gapopen" type="integer" optional="True" value="" label="Gap open penalty" help="leave empty for default (see scoring matrix)" />
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204 <param argument="--gapextend" type="integer" optional="True" value="" label="Gap extension penalty" help="leave empty for default (see scoring matrix)" />
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205 <param argument="--masking" type="boolean" truevalue="1" falsevalue="0" checked="true" label="enable masking of low complexity regions?" help="Masked residues appear in the output as X"/>
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206 <conditional name="tax_cond">
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207 <param name="tax_select" type="select" label="Restrict search taxonomically?" help="Any taxonomic rank can be used, and only reference sequences matching one of the specified taxon ids will be searched against">
7
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208 <option value="no" selected="True">No</option>
6
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209 <option value="list">list of taxids entered manually</option>
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210 <option value="file">list of taxids from single column tabular file</option>
1
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parents: 0
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211 </param>
6
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212 <when value="no"/>
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213 <when value="list">
8
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214 <param name="taxonlist" argument="--taxonlist" type="text" value="" label="comma separated list of taxon ids" help="">
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215 <validator type="regex" message="taxonlist needs to be a comma separated list of integers">[0-9,]*</validator>
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216 <validator type="expression" message="taxon ids 0 and 1 are not allowed">not ("0" in value.split(",") or "1" in value.split(","))</validator>
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parents: 7
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217 </param>
1
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parents: 0
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218 </when>
6
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219 <when value="file">
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220 <param name="taxonlistfile" argument="--taxonlist" type="data" format="tabular" label="Keep alignments within the given percentage range of the top alignment score for a quer" help="" />
1
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parents: 0
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221 </when>
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222 </conditional>
0
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223 <conditional name="filter_score">
1
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224 <param name="filter_score_select" type="select" label="Method to filter?" help="(--evalue/--min-score)">
7
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225 <option value="evalue" selected="True">Maximum e-value to report alignments</option>
1
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226 <option value="min-score">Minimum bit score to report alignments</option>
0
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227 </param>
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228 <when value="evalue">
1
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229 <param argument="--evalue" type="float" value="0.001" label="Maximum expected value to keep an alignment" />
0
98037ef3d2a9 Imported from capsule None
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230 </when>
1
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231 <when value="min-score">
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232 <param name="min_score" argument="--min-score" type="integer" value="0" label="Minimum bit score to keep an alignment" help="(--min-score)" />
0
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233 </when>
98037ef3d2a9 Imported from capsule None
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234 </conditional>
6
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235 <expand macro="hit_filter_macro" />
1
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236 <param argument="--id" type="integer" value="0" label="Minimum identity percentage to report an alignment" help="" />
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237 <param name="query_cover" argument="--query-cover" type="integer" value="0" label="Minimum query cover percentage to report an alignment" help="" />
6
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238 <param name="subject_cover" argument="--subject-cover" type="integer" value="0" label="Minimum subject cover percentage to report an alignment" help="" />
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239 <param argument="--unal" type="boolean" truevalue="1" falsevalue="0" checked="false" label="report unaligned queries" help=""/>
1
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240 </inputs>
0
98037ef3d2a9 Imported from capsule None
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241 <outputs>
6
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242 <expand macro="output_macro" />
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243 <data format="fasta" name="unalqueries" label="${tool.name} on ${on_string} (unaligned queries)">
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244 <filter>unal == "1"</filter>
1
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245 </data>
0
98037ef3d2a9 Imported from capsule None
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246 </outputs>
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247 <tests>
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248 <test>
6
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249 <conditional name="method_cond">
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250 <param name="method_select" value="blastp" />
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251 </conditional>
0
98037ef3d2a9 Imported from capsule None
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252 <param name="query" value="protein.fasta" ftype="fasta"/>
6
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253 <conditional name="ref_db_source">
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254 <param name="db_source" value="history"/>
8
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255 <param name="reference_database" value="db-wtax.dmnd"/>
6
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256 </conditional>
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257 <conditional name="output">
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258 <param name="outfmt" value="6"/>
8
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parents: 7
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259 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,cigar,scovhsp,sskingdoms,skingdoms,sphylums"/>
6
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260 </conditional>
8
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261 <conditional name="sens_cond">
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262 <param name="sensitivity" value=""/>
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263 </conditional>
1
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264 <param name="matrix" value="BLOSUM62"/>
6
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265 <param name="comp-based-stat" value="1"/>
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266 <param name="masking" value="1"/>
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267 <conditional name="hit_filter">
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268 <param name="hit_filter_select" value="max"/>
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269 <param name="max_target_seqs" value="25" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
270 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
271 <conditional name="filter_score">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
272 <param name="filter_score_select" value="evalue"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
273 <param name="evalue" value="0.001" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
274 </conditional>
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
275 <param name="id" value="0"/>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
276 <param name="query_cover" value="0"/>
8
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
parents: 7
diff changeset
277 <conditional name="sens_cond">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
parents: 7
diff changeset
278 <param name="block_size" value="2"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
parents: 7
diff changeset
279 </conditional>
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
280 <output name="blast_tabular" file="diamond_results.tabular"/>
0
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
281 </test>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
282 <test>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
283 <conditional name="method_cond">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
284 <param name="method_select" value="blastp" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
285 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
286 <param name="query" value="protein.fasta" ftype="fasta"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
287 <conditional name="ref_db_source">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
288 <param name="db_source" value="history"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
289 <param name="reference_database" value="db-wtax.dmnd"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
290 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
291 <conditional name="tax_cond">
8
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
parents: 7
diff changeset
292 <param name="tax_select" value="list"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
parents: 7
diff changeset
293 <param name="taxonlist" value="2" />
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
294 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
295 <conditional name="output">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
296 <param name="outfmt" value="6"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
297 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
298 </conditional>
8
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
parents: 7
diff changeset
299 <conditional name="sens_cond">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
parents: 7
diff changeset
300 <param name="sensitivity" value=""/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
parents: 7
diff changeset
301 </conditional>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
302 <param name="matrix" value="BLOSUM62"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
303 <param name="comp-based-stat" value="1"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
304 <param name="masking" value="1"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
305 <conditional name="hit_filter">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
306 <param name="hit_filter_select" value="max"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
307 <param name="max_target_seqs" value="25" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
308 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
309 <conditional name="filter_score">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
310 <param name="filter_score_select" value="evalue"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
311 <param name="evalue" value="0.001" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
312 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
313 <param name="id" value="0"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
314 <param name="query_cover" value="0"/>
8
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
parents: 7
diff changeset
315 <conditional name="sens_cond">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
parents: 7
diff changeset
316 <param name="block_size" value="2"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
parents: 7
diff changeset
317 </conditional>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
318 <output name="blast_tabular" file="diamond_results.wtax.tabular"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
319 </test>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
320 <test>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
321 <conditional name="method_cond">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
322 <param name="method_select" value="blastx" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
323 <conditional name="frameshift_cond">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
324 <param name="frameshift_select" value="yes"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
325 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
326 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
327 <param name="query" value="nucleotide.fasta" ftype="fasta"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
328 <conditional name="ref_db_source">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
329 <param name="db_source" value="history"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
330 <param name="reference_database" value="db.dmnd"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
331 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
332 <conditional name="output">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
333 <param name="outfmt" value="0"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
334 </conditional>
8
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
parents: 7
diff changeset
335 <conditional name="sens_cond">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
parents: 7
diff changeset
336 <param name="sensitivity" value=""/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
parents: 7
diff changeset
337 </conditional>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
338 <param name="matrix" value="BLOSUM62"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
339 <param name="comp-based-stat" value="1"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
340 <param name="masking" value="1"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
341 <conditional name="hit_filter">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
342 <param name="hit_filter_select" value="top"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
343 <param name="top" value="10" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
344 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
345 <conditional name="filter_score">
8
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
parents: 7
diff changeset
346 <param name="filter_score_select" value="min-score"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
parents: 7
diff changeset
347 <param name="min_score" value="1" />
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
348 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
349 <param name="id" value="0"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
350 <param name="query_cover" value="0"/>
8
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
parents: 7
diff changeset
351 <conditional name="sens_cond">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
parents: 7
diff changeset
352 <param name="block_size" value="2"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
parents: 7
diff changeset
353 </conditional>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
354 <output name="blast_tabular" file="diamond_results.pairwise"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
355 </test>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
356 <test>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
357 <conditional name="method_cond">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
358 <param name="method_select" value="blastp" />
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359 </conditional>
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360 <param name="query" value="protein.fasta" ftype="fasta"/>
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361 <conditional name="ref_db_source">
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362 <param name="db_source" value="history"/>
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363 <param name="reference_database" value="db-wtax.dmnd"/>
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364 </conditional>
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365 <conditional name="output">
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366 <param name="outfmt" value="100"/>
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367 </conditional>
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368 <output name="daa_output" file="diamond_results.daa" compare="sim_size" delta="10"/>
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369 </test>
8
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370 <test>
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371 <conditional name="method_cond">
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372 <param name="method_select" value="blastx" />
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373 <conditional name="frameshift_cond">
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374 <param name="frameshift_select" value="yes"/>
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375 </conditional>
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376 </conditional>
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377 <param name="query" value="nucleotide.fasta" ftype="fasta"/>
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378 <conditional name="ref_db_source">
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379 <param name="db_source" value="indexed"/>
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380 <param name="index" value="testDb"/>
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381 </conditional>
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382 <conditional name="output">
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parents: 7
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383 <param name="outfmt" value="0"/>
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384 </conditional>
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385 <conditional name="sens_cond">
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386 <param name="sensitivity" value=""/>
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387 </conditional>
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388 <param name="matrix" value="BLOSUM62"/>
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389 <param name="comp-based-stat" value="1"/>
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390 <param name="masking" value="1"/>
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parents: 7
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391 <conditional name="hit_filter">
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392 <param name="hit_filter_select" value="top"/>
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393 <param name="top" value="10" />
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394 </conditional>
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395 <conditional name="filter_score">
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396 <param name="filter_score_select" value="min-score"/>
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397 <param name="min_score" value="1" />
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398 </conditional>
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399 <param name="id" value="0"/>
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400 <param name="query_cover" value="0"/>
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parents: 7
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401 <conditional name="sens_cond">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
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402 <param name="block_size" value="2"/>
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403 </conditional>
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404 <output name="blast_tabular" file="diamond_results.pairwise"/>
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405 </test>
0
98037ef3d2a9 Imported from capsule None
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406 </tests>
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407 <help>
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408 <![CDATA[
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409
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410 **What it does**
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411
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412 DIAMOND_ is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.
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413 On Illumina reads of length 100-150bp, in fast mode, DIAMOND is about 20,000 times faster than BLASTX, while reporting
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414 about 80-90% of all matches that BLASTX finds, with an e-value of at most 1e-5. In sensitive mode, DIAMOND ist about 2,500
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415 times faster than BLASTX, finding more than 94% of all matches.
98037ef3d2a9 Imported from capsule None
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416
3
830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0
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417 The DIAMOND algorithm is designed for the alignment of large datasets. The algorithm is not efficient for a small number of query sequences or only a single one of them, and speed will be low. BLAST is recommended for small datasets.
1
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418
0
98037ef3d2a9 Imported from capsule None
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419 .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/
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420
1
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421 **Input**
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422
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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423 Input data is a large protein or nucleotide sequence file.
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424
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425
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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426 **Output**
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427
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428 Diamond gives you a tabular output file with 12 columns:
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429
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430 Column Description
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431 1 Query Seq-id (ID of your sequence)
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432 2 Subject Seq-id (ID of the database hit)
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433 3 Percentage of identical matches
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434 4 Alignment length
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435 5 Number of mismatches
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436 6 Number of gap openings
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437 7 Start of alignment in query
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438 8 End of alignment in query
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439 9 Start of alignment in subject (database hit)
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440 10 End of alignment in subject (database hit)
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441 11 Expectation value (E-value)
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442 12 Bit score
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443
0
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444
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445 Supported values for gap open and gap extend parameters depending on the selected scoring matrix.
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446
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447 ======== ============================================
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448 Matrix Supported values for (gap open)/(gap extend)
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449 ======== ============================================
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450 BLOSUM45 (10-13)/3; (12-16)/2; (16-19)/1
98037ef3d2a9 Imported from capsule None
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451 BLOSUM50 (9-13)/3; (12-16)/2; (15-19)/1
98037ef3d2a9 Imported from capsule None
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452 BLOSUM62 (6-11)/2; (9-13)/1
98037ef3d2a9 Imported from capsule None
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453 BLOSUM80 (6-9)/2; 13/2; 25/2; (9-11)/1
98037ef3d2a9 Imported from capsule None
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454 BLOSUM90 (6-9)/2; (9-11)/1
98037ef3d2a9 Imported from capsule None
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455 PAM250 (11-15)/3; (13-17)/2; (17-21)/1
98037ef3d2a9 Imported from capsule None
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456 PAM70 (6-8)/2; (9-11)/1
98037ef3d2a9 Imported from capsule None
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457 PAM30 (5-7)/2; (8-10)/1
98037ef3d2a9 Imported from capsule None
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458 ======== ============================================
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459
98037ef3d2a9 Imported from capsule None
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460
98037ef3d2a9 Imported from capsule None
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461 ]]>
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462 </help>
1
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463 <expand macro="citations" />
0
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464 </tool>