Mercurial > repos > iuc > megan_daa2info

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 5386f7bb4bf5bdd4b5303d0686c97fe5d9b99ca0"
author iuc
date Sat, 11 Dec 2021 11:51:12 +0000
parents 2f8df8e575f2
children
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2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
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1 <tool id="megan_daa2info" name="MEGAN: Get information" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>about a DIAMOND file</description>
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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="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 #set input_identifier = 'input.' + $input.ext.upper()
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10 ln -s '${input}' '${input_identifier}' &&
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11
2f8df8e575f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
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12 daa2info
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13 --in '${input_identifier}'
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14 #if str($input_is_meganized_cond.input_is_meganized) == 'yes':
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15 --listMore
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16 #if str($input_is_meganized_cond.list_class2count_cond.list_class2count) == 'yes':
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17 --class2count '$input_is_meganized_cond.list_class2count_cond.class2count'
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18 $input_is_meganized_cond.list_class2count_cond.sum
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19 #end if
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20 #if str($input_is_meganized_cond.list_read2class_cond.list_read2class) == 'yes':
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21 --read2class '$input_is_meganized_cond.list_read2class_cond.read2class'
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22 #end if
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23 $input_is_meganized_cond.names
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24 $input_is_meganized_cond.paths
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25 $input_is_meganized_cond.prefixRank
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26 $input_is_meganized_cond.majorRanksOnly
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27 #if str($input_is_meganized_cond.bo_or_vo) != 'do_not_restrict':
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28 $input_is_meganized_cond.bo_or_vo
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29 #end if
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30 $input_is_meganized_cond.ignoreUnassigned
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31 #else:
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32 --list
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33 #end if
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34 #if $extractSummaryFile:
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35 --extractSummaryFile '$output_summary'
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36 #end if
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37 --out '${output}'
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38 ]]></command>
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39 <inputs>
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40 <param name="input" argument="--in" type="data" format="daa" label="Input DIAMOND file"/>
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41 <conditional name="input_is_meganized_cond">
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42 <param name="input_is_meganized" type="select" checked="false" label="Input is meganized?" help="Implies the input file was produced by the MEGAN: DAA Meganizer tool">
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43 <option value="no" selected="true">No</option>
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44 <option value="yes">Yes</option>
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45 </param>
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46 <when value="no"/>
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47 <when value="yes">
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48 <conditional name="list_class2count_cond">
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49 <param name="list_class2count" type="select" label="List class to count for named classification(s)?">
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50 <option value="no" selected="true">No</option>
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51 <option value="yes">Yes</option>
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52 </param>
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53 <when value="no"/>
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54 <when value="yes">
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55 <param argument="--class2count" type="select" label="Select class to count for named classification(s)">
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56 <expand macro="classification_options"/>
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57 </param>
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58 <param argument="--sum" type="boolean" truevalue="--sum" falsevalue="" checked="false" label="Use summarized rather than assigned counts when listing class to count?"/>
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59 </when>
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60 </conditional>
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61 <conditional name="list_read2class_cond">
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62 <param name="list_read2class" type="boolean" truevalue="true" falsevalue="false" checked="false" label="List read to class assignments for named classification(s)?"/>
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63 <when value="false"/>
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64 <when value="true">
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65 <param argument="--read2class" type="select" label="Select read to class assignments for named classification(s)">
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66 <expand macro="classification_options"/>
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67 </param>
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68 </when>
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69 </conditional>
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70 <param argument="--names" type="boolean" truevalue="--names" falsevalue="" checked="false" label="Report class names rather than class Id numbers?"/>
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71 <param argument="--paths" type="boolean" truevalue="--paths" falsevalue="" checked="false" label="Report class paths rather than class Id numbers?"/>
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72 <param argument="--prefixRank" type="boolean" truevalue="--prefixRank" falsevalue="" checked="false" label="When reporting class paths for taxonomy, prefix single letter to indicate taxonomic rank?"/>
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73 <param argument="--majorRanksOnly" type="boolean" truevalue="--majorRanksOnly" falsevalue="" checked="false" label="Only use major taxonomic ranks?"/>
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74 <param name="bo_or_vo" type="select" label="Restrict reporting to either bacterial reads or viral reads in taxonomic report">
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75 <option value="do_not_restrict" selected="true">Do not restrict</option>
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76 <option value="--bacteriaOnly" selected="true">Bacterial reads and counts</option>
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77 <option value="--virusOnly">Viral reads and counts</option>
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78 </param>
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79 <param argument="--ignoreUnassigned" type="boolean" truevalue="--ignoreUnassigned" falsevalue="" checked="true" label="Don't report on reads that are unassigned?"/>
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80 </when>
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81 </conditional>
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82 <param argument="--extractSummaryFile" type="boolean" truevalue="--extractSummaryFile" falsevalue="" checked="false" label="Output a MEGAN summary file?" help="Contains all classifications, but no reads or alignments"/>
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83 </inputs>
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84 <outputs>
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85 <data name="output" format="txt"/>
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86 <data name="output_summary" format="txt" label="${tool.name} on ${on_string} (MEGAN summary)">
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87 <filter>extractSummaryFile</filter>
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88 </data>
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89 </outputs>
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90 <tests>
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91 <test expect_num_outputs="1">
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92 <param name="input" value="input.daa" ftype="daa"/>
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93 <output name="output" file="daa2info_output1.txt" ftype="txt" compare="contains"/>
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94 </test>
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95 <test expect_num_outputs="1">
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96 <param name="input" value="input_meganized.daa" ftype="daa"/>
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97 <param name="input_is_meganized" value="yes"/>
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98 <output name="output" file="daa2info_output2.txt" ftype="txt" compare="contains"/>
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99 </test>
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100 <test expect_num_outputs="2">
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101 <param name="input" value="input_meganized.daa" ftype="daa"/>
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102 <param name="input_is_meganized" value="yes"/>
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103 <param name="bo_or_vo" value="--virusOnly"/>
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104 <param name="extractSummaryFile" value="true"/>
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105 <output name="output" file="daa2info_output2.txt" ftype="txt" compare="contains"/>
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106 <output name="output_summary" file="daa2info_output_summary2.txt" ftype="txt" compare="contains"/>
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107 </test>
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108 </tests>
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109 <help>
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110 **What it does**
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111
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112 Analyses a DIAMOND (i.e., a Direct Access Archive or DAA) file, a proprietary file format developed by PowerISO Computing
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113 for disk image files, and outputs a text file containing information about the file. The information includes the following.
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114
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115 * Number of reads
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116 * Alignment mode
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117 * Whether the file is meganized
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118 * Classifications
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119
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120 If the DIAMOND file is meganized (i.e., it was produced by the MEGAN: DAA Meganizer tool), a summary that includes the
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121 following information (among other items) is included in the output.
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122
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123 * Content type
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124 * Names
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125 * Uids
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126 * Sizes
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127 * Additional reads
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128 * Algorithm
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129 * Parameters
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130
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131 If the user elects to output a MEGAN summary file, an additional text file that includes the following information (among
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132 other items) is produced.
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133
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134 * Creator
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135 * Creation date
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136 * Content type
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137 * Blast mode
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138 * Uids
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139
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140 </help>
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141 <expand macro="citations"/>
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142 </tool>
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143