Mercurial > repos > iuc > qiime_pick_open_reference_otus

annotate pick_open_reference_otus.xml @ 0:f668a753bcfc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 03:55:46 -0400
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children 41482ca21d31
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f668a753bcfc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <tool id="qiime_pick_open_reference_otus" name="Perform open-reference OTU picking" version="@WRAPPER_VERSION@.0">
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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 <expand macro="requirements"/>
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7 <version_command>pick_open_reference_otus.py --version</version_command>
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8 <command detect_errors="aggressive"><![CDATA[
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9 pick_open_reference_otus.py
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10 --input_fps '$input_fps'
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11 -o otus
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12 --otu_picking_method '$otu_picking_method'
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13 #if str( $ref_sequences.selector ) == 'history'
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14 #set $ref = $ref_sequences.reference_fp
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15 #else:
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16 #set $ref = $ref_sequences.reference_fp.fields.path
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17 #end if
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18 --reference_fp '$ref'
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19 #if str( $prefilter.use_prefilter ) == 'yes'
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20 #if str( $prefilter.prefilter_ref_seq.selector ) == 'history'
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21 #set $ref = $prefilter.prefilter_ref_seq.prefilter_refseqs_fp
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22 #else:
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23 #set $ref = $prefilter.prefilter_ref_seq.prefilter_refseqs_fp.fields.path
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24 #end if
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25 --prefilter_refseqs_fp '$ref'
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26 #end if
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27 --new_ref_set_id '$new_ref_set_id'
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28 $parallel
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29 -O "\${GALAXY_SLOTS:-4}"
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30 --percent_subsample '$percent_subsample'
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31 --prefilter_percent_id '$prefilter_percent_id'
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32 #if str($step1_otu_map_fp) != 'None':
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33 --step1_otu_map_fp '$step1_otu_map_fp'
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34 #end if
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35 #if str($step1_failures_fasta_fp) != 'None':
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36 --step1_failures_fasta_fp='$step1_failures_fasta_fp'
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37 #end if
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38 --minimum_failure_threshold '$minimum_failure_threshold'
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39 $suppress_step4
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40 --min_otu_size '$min_otu_size'
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41 $suppress_taxonomy_assignment
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42 $suppress_align_and_tree
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43
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44 #if str( $suppress_align_and_tree ) == ""
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45 #if str( $suppress_taxonomy_assignment ) == ""
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46 && mv otus/otu_table_mc*_w_tax.biom otus/otu_table_w_tax.biom
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47 && mv otus/otu_table_mc*_w_tax_no_pynast_failures.biom otus/tu_table_w_tax_no_pynast_failures
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48 #else
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49 && mv otus/otu_table_mc*_no_pynast_failures.biom otus/otu_table_no_pynast_failures.biom
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50 #end if
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51 #end if
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52
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53 ]]></command>
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54 <inputs>
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55 <param argument="--input_fps" type="data" format="fasta,fastq" multiple="True" label="Input sequence files"/>
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56 <param argument="--otu_picking_method" type="select" label="The OTU picking method to use for reference and de novo steps">
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57 <option value="uclust" selected="True">uclust</option>
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58 </param>
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59 <conditional name="ref_sequences">
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60 <param name="selector" type="select" label="Reference sequences to query">
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61 <option value="cached" selected="True">Public databases</option>
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62 <option value="history">Databases from your history</option>
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63 </param>
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64 <when value="cached">
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65 <param argument="--reference_fp" label="Reference sequences" type="select">
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66 <options from_data_table="qiime_rep_set"/>
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67 </param>
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68 </when>
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69 <when value="history">
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70 <param argument="--reference_fp" type="data" format="fasta" label="Reference databases"/>
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71 </when>
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72 </conditional>
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73 <conditional name="prefilter">
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74 <param name="use_prefilter" type="select" label="Use different reference sequences for the prefilter?">
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75 <option value="true">True</option>
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76 <option value="false" selected="True">False</option>
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77 </param>
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78 <when value="true">
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79 <conditional name="prefilter_ref_seq">
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80 <param name="selector" type="select" label="Reference sequences to query">
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81 <option value="cached" selected="True">Public databases</option>
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82 <option value="history">Databases from your history</option>
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83 </param>
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84 <when value="cached">
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85 <param argument="--prefilter_refseqs_fp" label="Reference sequences" type="select">
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86 <options from_data_table="qiime_rep_set"/>
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87 </param>
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88 </when>
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89 <when value="history">
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90 <param argument="--prefilter_refseqs_fp" type="data" format="fasta" label="Reference databases"/>
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91 </when>
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92 </conditional>
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93 </when>
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94 <when value="false"/>
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95 </conditional>
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96 <param argument="--new_ref_set_id" type="text" value="New" label="Unique identifier for OTUs that get created in this ref set" help="This is useful to support combining of reference sets"/>
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97 <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="False" label="Run in parallel where available?"/>
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98 <param argument="--percent_subsample" type="float" value="0.001" min="0" max="1" label="Percent of failure sequences to include in the subsample to cluster de novo" help="Large numbers should give more comprehensive results but will be slower"/>
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99 <param argument="--prefilter_percent_id" type="float" value="0.0" min="0" max="1" label="Percent of sequence pre-cluster against the reference" help="Any reads which fail to hit are discarded (a quality filter)"/>
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100 <param argument="--step1_otu_map_fp" type="data" format="txt" optional="True" label="Reference OTU picking OTU map to avoid rebuilding if one has already been built (optional)" help="This must be an OTU map generated by this workflow, not (for example) by pick_closed_reference_otus"/>
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101 <param argument="--step1_failures_fasta_fp" type="data" format="fasta" optional="True" label="Reference OTU picking failures fasta filepath, to avoid rebuilding if one has already been built (optional)" help="This must be a failures file generated by this workflow, not (for example) by pick_closed_reference_otus"/>
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102 <param argument="--minimum_failure_threshold" type="integer" value="100000" label="Minimum number of sequences that must fail to hit the reference for subsampling to be performed" help="If fewer than this number of sequences fail to hit the reference, the de novo clustering step will run serially rather than invoking the subsampled open reference approach to improve performance"/>
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103 <param argument="--suppress_step4" type="boolean" truevalue="--suppress_step4" falsevalue="" checked="False" label="Suppress the final de novo OTU picking step?" help="It may be necessary for extremely large data sets"/>
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104 <param argument="--min_otu_size" type="integer" value="2" label="Minimum otu size to retain the OTU" help=""/>
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105 <param argument="--suppress_taxonomy_assignment" type="boolean" truevalue="--suppress_taxonomy_assignment" falsevalue="" checked="False" label="Skip the taxonomy assignment step?" help="It results in an OTU table without taxonomy"/>
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106 <param argument="--suppress_align_and_tree" type="boolean" truevalue="--suppress_align_and_tree" falsevalue="" checked="False" label="Skip the sequence alignment and tree-building steps?" help=""/>
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107 </inputs>
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108 <outputs>
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109 <data name="final_otu_map" format="txt" from_work_dir="otus/final_otu_map.txt" label="${tool.name} on ${on_string}: Final OTU map"/>
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110 <data name="final_otu_map_mc" format="txt" from_work_dir="otus/final_otu_map_mc*.txt" label="${tool.name} on ${on_string}: Final OTU map without the OTUs failing the minimum specified OTU size"/>
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111 <data name="rep_set" format="fasta" from_work_dir="otus/rep_set.fna" label="${tool.name} on ${on_string}: OTU representative sequences"/>
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112 <data name="otu_table_mc" format="biom1" from_work_dir="otus/otu_table_mc*.biom" label="${tool.name} on ${on_string}: OTU table"/>
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113 <data name="otu_table_mc_w_tax" format="biom1" from_work_dir="otus/otu_table_w_tax.biom" label="${tool.name} on ${on_string}: OTU table with taxonomic assignment">
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114 <filter>suppress_taxonomy_assignment is False</filter>
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115 </data>
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116 <data name="otu_table_mc_w_tax_no_pynast_failures" format="biom1" from_work_dir="otus/otu_table_w_tax_no_pynast_failures.biom" label="${tool.name} on ${on_string}: OTU table with taxonomic assignment and without sequences failing the alignment to the OTU representative sequences">
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117 <filter>suppress_taxonomy_assignment is False and suppress_align_and_tree is False</filter>
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118 </data>
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119 <data name="otu_table_mc_no_pynast_failures" format="biom1" from_work_dir="otus/otu_table_no_pynast_failures.biom" label="${tool.name} on ${on_string}: OTU table without sequences failing the alignment to the OTU representative sequences">
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120 <filter>suppress_taxonomy_assignment is True and suppress_align_and_tree is False</filter>
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121 </data>
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122 <data name="rep_set_tree" format="txt" from_work_dir="otus/rep_set.tre" label="${tool.name} on ${on_string}: Representative set tree">
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123 <filter>suppress_align_and_tree is False</filter>
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124 </data>
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125 <data name="new_refseqs" format="fasta" from_work_dir="otus/new_refseqs.fna" label="${tool.name} on ${on_string}: New reference sequences (OTU + input reference sequences)"/>
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126 </outputs>
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127 <tests>
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128 <test>
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129 <param name="input_fps" value="pick_open_reference_otus/sequences.fasta"/>
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130 <param name="otu_picking_method" value="uclust"/>
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131 <conditional name="ref_sequences">
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132 <param name="selector" value="history"/>
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133 <param name="reference_fp" value="pick_open_reference_otus/gg_13_8_79_otus.fasta"/>
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134 </conditional>
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135 <conditional name="prefilter">
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136 <param name="use_prefilter" value="false"/>
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137 </conditional>
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138 <param name="new_ref_set_id" value="New"/>
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139 <param name="parallel" value="--parallel"/>
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140 <param name="percent_subsample" value="0.001"/>
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141 <param name="prefilter_percent_id" value="0.0"/>
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142 <param name="minimum_failure_threshold" value="100000"/>
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143 <param name="suppress_step4" value=""/>
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144 <param name="min_otu_size" value="2"/>
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145 <param name="suppress_taxonomy_assignment" value=""/>
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146 <param name="suppress_align_and_tree" value=""/>
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147 <output name="final_otu_map" value="pick_open_reference_otus/1_final_otu_map.txt"/>
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148 <output name="final_otu_map_mc" value="pick_open_reference_otus/1_final_otu_map_mc.txt"/>
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149 <output name="rep_set">
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150 <assert_contents>
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151 <has_line line=">4374484 L1S8_76"></has_line>
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152 <has_text text=">New.CleanUp.ReferenceOTU6 L1S208_7"></has_text>
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153 </assert_contents>
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154 </output>
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155 <output name="rep_set_tree" value="pick_open_reference_otus/1_rep_set_tree.tre"/>
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156 <output name="new_refseqs">
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157 <assert_contents>
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158 <has_line line=">1109493"></has_line>
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159 <has_text text=">945028"></has_text>
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160 <has_text text=">4437874"></has_text>
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161 <has_text text=">New.CleanUp.ReferenceOTU6 L1S208_7"></has_text>
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162 </assert_contents>
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163 </output>
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164 </test>
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165 <test>
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166 <param name="input_fps" value="pick_open_reference_otus/sequences.fasta"/>
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167 <param name="otu_picking_method" value="uclust"/>
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168 <conditional name="ref_sequences">
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169 <param name="selector" value="history"/>
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170 <param name="reference_fp" value="pick_open_reference_otus/gg_13_8_79_otus.fasta"/>
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171 </conditional>
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172 <conditional name="prefilter">
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173 <param name="use_prefilter" value="false"/>
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174 </conditional>
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175 <param name="new_ref_set_id" value="New"/>
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176 <param name="parallel" value="--parallel"/>
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177 <param name="percent_subsample" value="0.001"/>
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178 <param name="prefilter_percent_id" value="0.0"/>
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179 <param name="minimum_failure_threshold" value="100000"/>
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180 <param name="suppress_step4" value=""/>
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181 <param name="min_otu_size" value="3"/>
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182 <param name="suppress_taxonomy_assignment" value="--suppress_taxonomy_assignment"/>
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183 <param name="suppress_align_and_tree" value="--suppress_align_and_tree"/>
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184 <output name="final_otu_map" value="pick_open_reference_otus/2_final_otu_map.txt"/>
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185 <output name="final_otu_map_mc" value="pick_open_reference_otus/2_final_otu_map_mc.txt"/>
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186 <output name="rep_set">
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187 <assert_contents>
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188 <has_line line=">4374484 L1S8_76"></has_line>
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189 <has_text text=">New.CleanUp.ReferenceOTU6 L1S208_7"></has_text>
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190 </assert_contents>
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191 </output>
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192 <output name="new_refseqs">
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193 <assert_contents>
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194 <has_line line=">1109493"></has_line>
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195 <has_text text=">945028"></has_text>
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196 <has_text text=">4437874"></has_text>
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197 <has_text text=">New.CleanUp.ReferenceOTU6 L1S208_7"></has_text>
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198 </assert_contents>
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199 </output>
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200 </test>
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201 <test>
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202 <param name="input_fps" value="pick_open_reference_otus/sequences.fasta"/>
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203 <param name="otu_picking_method" value="uclust"/>
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204 <conditional name="ref_sequences">
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205 <param name="selector" value="history"/>
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206 <param name="reference_fp" value="pick_open_reference_otus/gg_13_8_79_otus.fasta"/>
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207 </conditional>
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208 <conditional name="prefilter">
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209 <param name="use_prefilter" value="false"/>
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210 </conditional>
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211 <param name="new_ref_set_id" value="New"/>
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212 <param name="parallel" value="--parallel"/>
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213 <param name="percent_subsample" value="0.001"/>
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214 <param name="prefilter_percent_id" value="0.0"/>
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215 <param name="minimum_failure_threshold" value="100000"/>
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216 <param name="suppress_step4" value=""/>
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217 <param name="min_otu_size" value="10"/>
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218 <param name="suppress_taxonomy_assignment" value="--suppress_taxonomy_assignment"/>
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219 <param name="suppress_align_and_tree" value=""/>
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220 <output name="final_otu_map" value="pick_open_reference_otus/3_final_otu_map.txt"/>
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221 <output name="final_otu_map_mc" value="pick_open_reference_otus/3_final_otu_map_mc.txt"/>
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222 <output name="rep_set">
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223 <assert_contents>
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224 <has_line line=">New.CleanUp.ReferenceOTU20 L1S8_4"></has_line>
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225 <has_text text=">New.CleanUp.ReferenceOTU21 L1S140_45"></has_text>
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226 <has_text text=">New.CleanUp.ReferenceOTU22 L1S208_15"></has_text>
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227 </assert_contents>
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228 </output>
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229 <output name="rep_set_tree" value="pick_open_reference_otus/3_rep_set_tree.tre"/>
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230 <output name="new_refseqs">
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231 <assert_contents>
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232 <has_line line=">1109493"></has_line>
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233 <has_text text=">945028"></has_text>
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234 <has_text text=">4431138"></has_text>
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235 <has_text text=">New.CleanUp.ReferenceOTU22 L1S208_15"></has_text>
f668a753bcfc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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236 </assert_contents>
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237 </output>
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238 </test>
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239 </tests>
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240 <help><![CDATA[
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241 **What it does**
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242
f668a753bcfc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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243 This tool performs open-reference OTU picking from sequences.
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244
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245 This script is broken down into 4 possible OTU picking steps, and 2 steps
f668a753bcfc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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246 involving the creation of OTU tables and trees.
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247
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248 More information about this tool is available on
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249 `QIIME documentation <http://qiime.org/scripts/pick_open_reference_otus.html>`_.
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250 ]]></help>
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251 <citations>
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252 <expand macro="citations"/>
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253 </citations>
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254 </tool>