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annotate kma_map.xml @ 3:d9bc3ec3a710 draft default tip

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author dfornika
date Wed, 05 Feb 2020 00:58:24 +0000
parents 1c1dba36c061
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3
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1 <tool id="kma_map" name="Map with KMA" version="@TOOL_VERSION@_galaxy0">
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2 <description></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 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">kma</requirement>
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8 </requirements>
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9 <version_command>kma -v</version_command>
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10 <command detect_errors="exit_code">
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11 <![CDATA[
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12 kma
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13 -t \${GALAXY_SLOTS:-1}
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14 -t_db '${kma_index.fields.path}'
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15 #if $single_paired.single_paired_selector == 'yes'
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16 -ipe '${single_paired.forward_input}' '${single_paired.reverse_input}'
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17 #elif $single_paired.single_paired_selector == "collection":
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18 -ipe '${single_paired.input_pair.forward}' '${single_paired.input_pair.reverse}'
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19 #else:
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20 -i '${single_paired.input_sequences}'
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21 #end if
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22 #if str($settings.advanced) == "advanced"
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23 #if str($settings.kmer_size)
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24 -k '${settings.kmer_size}'
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25 #end if
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26 #if str($settings.p_value)
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27 -p '${settings.p_value}'
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28 #end if
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29 ${settings.decontaminate}
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30 ${settings.dense}
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31 ${settings.ref_fsa}
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32 ${settings.matrix}
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33 ${settings.all_best_mappings}
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34 #if str($settings.minimum_phred_score)
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35 -mp '${settings.minimum_phred_score}'
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36 #end if
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37 #if str($settings.cut_5_prime)
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38 -5p '${settings.cut_5_prime}'
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39 #end if
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40 ${settings.only_count_kmers}
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41 #if str($settings.min_id)
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42 -ID '${settings.min_id}'
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43 #end if
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44 ${settings.force_end_to_end}
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45 #end if
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46 -o output
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47
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48 #if str($settings.advanced) == "advanced" and $settings.matrix
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49 && gunzip output.mat.gz
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50 #end if
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51 && gunzip output.frag.gz
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52 ]]>
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53 </command>
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54 <inputs>
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55 <conditional name="single_paired">
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56 <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
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57 <option value="collection">Collection</option>
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58 <option value="yes">Paired</option>
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59 <option selected="True" value="no">Single</option>
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60 </param>
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61 <when value="collection">
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62 <param format="fastq" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTQ datasets" />
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63 </when>
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64 <when value="yes">
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65 <param format="fastq" name="forward_input" type="data" label="Forward strand" help="FASTQ dataset"/>
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66 <param format="fastq" name="reverse_input" type="data" label="Reverse strand" help="FASTQ dataset"/>
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67 </when>
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68 <when value="no">
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69 <param format="fastq" label="Input sequences" name="input_sequences" type="data" help="FASTQ datasets"/>
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70 </when>
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71 </conditional>
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72
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73 <param name="kma_index" type="select">
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74 <options from_data_table="kma_index">
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75 <validator type="no_options" message="No KMA index available" />
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76 </options>
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77 </param>
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78
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79 <conditional name="settings">
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80 <param name="advanced" type="select" label="Specify advanced parameters">
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81 <option value="simple" selected="true">No, use program defaults.</option>
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82 <option value="advanced">Yes, see full parameter list.</option>
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83 </param>
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84 <when value="simple">
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85 </when>
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86 <when value="advanced">
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87 <param name="kmer_size" type="integer" min="4" value="16" max="32" label="Kmer Size" />
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88 <param name="p_value" type="float" min="0.0" value="0.05" max="1.0" label="p-value"/>
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89 <param name="exhaustive_mode" type="boolean" truevalue="-ex_mode" falsevalue="" label="Exhaustive Mode" />
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90 <param name="decontaminate" type="boolean" truevalue="-deCon" falsevalue="" label="Decontaminate" />
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91 <param name="dense" type="boolean" truevalue="-dense" falsevalue="" label="Do not allow insertions in assembly" />
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92 <param name="ref_fsa" type="boolean" truevalue="-ref_fsa" falsevalue="" label="Consensus sequence has 'n' instead of gaps" />
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93 <param name="matrix" type="boolean" truevalue="-matrix" falsevalue="" label="Print assembly matrix" />
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94 <param name="all_best_mappings" type="boolean" truevalue="-a" falsevalue="" label="Print all best mappings" />
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95 <param name="minimum_phred_score" type="integer" min="0" value="20" max="60" label="Minimum phred score" />
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96 <param name="cut_5_prime" type="integer" min="0" value="0" max="64" label="Cut a constant number of nucleotides from the 5 prime" />
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97 <param name="only_count_kmers" type="boolean" truevalue="-Sparse" falsevalue="" label="Only count kmers" />
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98 <param name="min_id" type="float" min="0.0" value="1.0" max="100.0" label="Minimum percent identity"/>
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99 <param name="force_end_to_end" type="boolean" truevalue="-1t1" falsevalue="" label="Force end to end mapping" />
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100 </when>
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101 </conditional>
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102 </inputs>
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103 <outputs>
1
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104 <data name="result_overview" label="Result overview" format="tabular" from_work_dir="output.res" />
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105 <data name="consensus_alignment" label="Consensus alignment" format="fasta" from_work_dir="output.aln" />
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106 <data name="consensus_sequences" label="Consensus sequences" format="fasta" from_work_dir="output.fsa" />
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107 <data name="read_mapping" label="Read mapping info" format="tabular" from_work_dir="output.frag" />
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108 <data name="assembly_matrix" label="Assembly matrix" format="txt" from_work_dir="output.mat">
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109 <filter>settings['matrix']</filter>
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110 </data>
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111 </outputs>
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112 <tests>
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113 <test>
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114 <param name="single_paired_selector" value="no"/>
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115 <param name="input_sequences" value="ERR884056_ecoli_b0842.mapped_R1.fastq" ftype="fastq"/>
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116 <param name="advanced" value="advanced"/>
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117 <param name="kmer_size" value="8"/>
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118 <param name="kma_index" value="test_index"/>
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119 <output name="result_overview" file="ERR884056.res" ftype="tabular"/>
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120 <output name="consensus_alignment" file="ERR884056.aln" ftype="fasta"/>
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121 <output name="consensus_sequences" file="ERR884056.fsa" ftype="fasta"/>
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122 <output name="read_mapping" file="ERR884056.frag" ftype="tabular"/>
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123 </test>
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124 <test>
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125 <param name="single_paired_selector" value="no"/>
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126 <param name="input_sequences" value="ERR884056_ecoli_b0842.mapped_R1.fastq" ftype="fastq"/>
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127 <param name="advanced" value="advanced"/>
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128 <param name="kmer_size" value="8"/>
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129 <param name="matrix" value="true"/>
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130 <param name="kma_index" value="test_index"/>
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131 <output name="assembly_matrix" file="ERR884056.mat" ftype="txt"/>
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132 </test>
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133 </tests>
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134 <help>
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135 <![CDATA[
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136 ]]>
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137 </help>
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138 <expand macro="citations" />
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139 </tool>