Mercurial > repos > galaxyp > percolator

annotate nested_collection.xml @ 3:d4b3842dc781 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b3873302e7bb7917a43b455875208e6e9fcf8f66
author galaxyp
date Sat, 08 Apr 2017 08:22:40 -0400
parents b20ea66c01f0
children 022f2c8d3274
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d4b3842dc781 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b3873302e7bb7917a43b455875208e6e9fcf8f66
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1 <tool id="batched_set_list_creator" name="Create nested list" version="3.2">
1
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2 <description>based on filenames and batch sizes</description>
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3 <stdio>
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4 <exit_code range="1:" />
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5 </stdio>
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6 <command>python $__tool_directory__/nested_collection.py
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7 #if $batchsize
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8 --batchsize $batchsize
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9 #end if
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10 #if len($poolids) > 0
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11 --pool-ids
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12 #for $pool in $poolids
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13 '${pool.pool_identifier}'
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14 #end for
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15 #end if
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16 --real-names
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17 #for $fname in $listtobatch.keys()
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18 '$fname'
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19 #end for
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20 --galaxy-files
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21 #for $fname in $listtobatch.keys()
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22 '$listtobatch[$fname]'
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23 #end for
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24 </command>
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25 <inputs>
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26 <param name="batchsize" type="integer" optional="true" value="" label="Maximal amount of fractions to batch." help="No value means no maximum" />
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27 <param name="filetype" type="select" label="Which datatype to nest?">
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28 <option value="mzid">mzIdentML</option>
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29 <option value="percout">Percolator out</option>
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30 <option value="tabular">Tabular</option>
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31 </param>
1
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32 <repeat name="poolids" title="Batch pools" help="Pools containing batches (optional, not using this will result in one pool)">
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33 <param name="pool_identifier" type="text" label="Filename part identifying batchpool"
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34 help="Specify part of the input filenames that are unique for each pool, e.g set_A. Do not use 3 consecutive underscores."/>
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35 </repeat>
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36 <param name="listtobatch" type="data_collection" collection_type="list" label="List of files to batch" />
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37 </inputs>
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38 <outputs>
3
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39 <collection name="batched_fractions_mzid" type="list:list" label="Pooled batched mzIdentML data">
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40 <filter>filetype == "mzid"</filter>
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41 <discover_datasets pattern="(?P&lt;identifier_0&gt;\w+[^_][^_][^_])___(?P&lt;identifier_1&gt;[^_]+)\.data" ext="mzid" visible="false" />
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42 </collection>
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43 <collection name="batched_fractions_perco" type="list:list" label="Pooled batched percolator data">
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44 <filter>filetype == "percout"</filter>
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45 <discover_datasets pattern="(?P&lt;identifier_0&gt;\w+[^_][^_][^_])___(?P&lt;identifier_1&gt;[^_]+)\.data" ext="percout" visible="false" />
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46 </collection>
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47 <collection name="batched_fractions_tab" type="list:list" label="Pooled batched tabular data">
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48 <filter>filetype == "tabular"</filter>
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49 <discover_datasets pattern="(?P&lt;identifier_0&gt;\w+[^_][^_][^_])___(?P&lt;identifier_1&gt;[^_]+)\.data" ext="tabular" visible="false" />
1
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50 </collection>
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51 </outputs>
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52 <tests>
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53 <test>
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54 <param name="batchsize" value="2"/>
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55 <param name="filetype" value="mzid" />
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56 <param name="listtobatch">
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57 <collection type="list">
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58 <element name="fraction_one_spectra" value="empty_file1.mzid"/>
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59 <element name="fraction_two_spectra" value="empty_file2.mzid"/>
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60 <element name="fraction_three_spectra" value="empty_file3.mzid"/>
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61 <element name="fraction_four_spectra" value="empty_file4.mzid"/>
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62 </collection>
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63 </param>
3
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64 <output_collection name="batched_fractions_mzid" type="list:list">
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65 <element name="pool0_batch0">
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66 <element name="inputfn0" ftype="mzid" file="empty_file1.mzid"/>
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67 <element name="inputfn1" ftype="mzid" file="empty_file2.mzid"/>
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68 </element>
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69 <element name="pool0_batch1">
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70 <element name="inputfn0" ftype="mzid" file="empty_file3.mzid"/>
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71 <element name="inputfn1" ftype="mzid" file="empty_file4.mzid"/>
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72 </element>
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73 </output_collection>
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74 </test>
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75 <test>
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76 <repeat name="poolids">
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77 <param name="pool_identifier" value="set1"/>
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78 </repeat>
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79 <repeat name="poolids">
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80 <param name="pool_identifier" value="set2"/>
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81 </repeat>
3
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82 <param name="filetype" value="tabular" />
1
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83 <param name="listtobatch">
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84 <collection type="list">
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85 <element name="fr_one_set1_spectra" value="empty_file1.mzid"/>
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86 <element name="fr_two_set1_spectra" value="empty_file2.mzid"/>
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87 <element name="fr_three_set1_spectra" value="empty_file3.mzid"/>
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88 <element name="fr_one_set2_spectra" value="empty_file4.mzid"/>
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89 <element name="fr_two_set2_spectra" value="empty_file5.mzid"/>
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90 <element name="fr_three_set2_spectra" value="empty_file6.mzid"/>
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91 </collection>
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92 </param>
3
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93 <output_collection name="batched_fractions_tab" type="list:list">
2
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94 <element name="set1_batch0">
3
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95 <element name="inputfn0" ftype="tabular" file="empty_file1.mzid"/>
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96 <element name="inputfn1" ftype="tabular" file="empty_file2.mzid"/>
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97 <element name="inputfn2" ftype="tabular" file="empty_file3.mzid"/>
1
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98 </element>
2
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99 <element name="set2_batch1">
3
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100 <element name="inputfn0" ftype="tabular" file="empty_file4.mzid"/>
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101 <element name="inputfn1" ftype="tabular" file="empty_file5.mzid"/>
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102 <element name="inputfn2" ftype="tabular" file="empty_file6.mzid"/>
1
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103 </element>
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104 </output_collection>
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105 </test>
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106 <test>
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107 <param name="batchsize" value="2"/>
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108 <repeat name="poolids">
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109 <param name="pool_identifier" value="set1"/>
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110 </repeat>
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111 <repeat name="poolids">
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112 <param name="pool_identifier" value="set2"/>
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113 </repeat>
3
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114 <param name="filetype" value="percout" />
1
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115 <param name="listtobatch">
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116 <collection type="list">
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117 <element name="fr_one_set1_spectra" value="empty_file1.mzid"/>
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118 <element name="fr_two_set1_spectra" value="empty_file2.mzid"/>
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119 <element name="fr_three_set1_spectra" value="empty_file3.mzid"/>
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120 <element name="fr_one_set2_spectra" value="empty_file4.mzid"/>
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121 <element name="fr_two_set2_spectra" value="empty_file5.mzid"/>
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122 <element name="fr_three_set2_spectra" value="empty_file6.mzid"/>
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123 </collection>
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124 </param>
3
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125 <output_collection name="batched_fractions_perco" type="list:list">
2
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126 <element name="set1_batch0">
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127 <element name="inputfn0" ftype="percout" file="empty_file1.mzid"/>
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128 <element name="inputfn1" ftype="percout" file="empty_file2.mzid"/>
1
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129 </element>
2
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130 <element name="set1_batch1">
3
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131 <element name="inputfn0" ftype="percout" file="empty_file3.mzid"/>
1
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132 </element>
2
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133 <element name="set2_batch2">
3
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134 <element name="inputfn0" ftype="percout" file="empty_file4.mzid"/>
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135 <element name="inputfn1" ftype="percout" file="empty_file5.mzid"/>
1
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136 </element>
2
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137 <element name="set2_batch3">
3
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138 <element name="inputfn0" ftype="percout" file="empty_file6.mzid"/>
1
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139 </element>
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140 </output_collection>
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141 </test>
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142 </tests>
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143 <help>
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144 Creates nested collection containing from a list containing datasets in batches of
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145 a specific size. Useful when e.g. creating inputs to sqt2pin, msgfplus2pin or tandem2pin.
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146 Use this feature when you want to batch a specific amount of datasets, or datasets with
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147 a common file name pattern, or both.
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148 The tool generates a collection containing batches which contain multiple batches
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149 of input files. The pools are specified as a pattern in the input
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150 files which makes sure the batching isn't continued through very different input sets
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151 if that is a problem. Instead, for each filename-pattern it generates batches of the
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152 specified size.
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153 </help>
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154 </tool>