Mercurial > repos > bgruening > split_file_to_collection

annotate split_file_to_collection.xml @ 0:e9d56b4c3209 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
author bgruening
date Tue, 17 Jul 2018 14:36:55 -0400
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children 6400d2b0175f
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e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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1 <tool id="split_file_to_collection" name="Split file" version="0.1.1">
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2 <description>to dataset collection</description>
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3 <macros>
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4 <xml name="numnew_fname">
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5 <param name="numnew" type="integer" label="Number of new files" min="1" value="1"/>
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6 <param name="newfilenames" type="text" label="Base name for new files in collection"
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7 help="This will increment automatically - if input is 'file', then output is 'file0', 'file1', etc." value="split_file"/>
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8 <conditional name="select_allocate">
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9 <param name="allocate" type="select" label="Method to allocate records to new files" help="See the information section for a diagram">
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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10 <option value="random">At random</option>
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11 <option value="batch">Maintain record order</option>
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12 <option value="byrow" selected="true">Alternate output files</option>
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13 </param>
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14 <when value="random">
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15 <param name="seed" type="integer" label="Random number seed" help="For reproducibility, set this to some arbitrary integer (i.e. '1010')" value="1010"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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16 </when>
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17 <when value="batch">
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18 </when>
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19 <when value="byrow">
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20 </when>
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21 </conditional>
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22 </xml>
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23 </macros>
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24 <requirements>
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25 <requirement type="package" version="3.5">python</requirement>
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26 </requirements>
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27 <command detect_errors="aggressive"><![CDATA[
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28 mkdir ./out &&
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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29 python '$__tool_directory__/split_file_to_collection.py'
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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30 --out ./out
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31 --in '$split_parms.input'
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32 --ftype '$split_parms.select_ftype'
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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33 #if $split_parms.select_ftype == "tabular":
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34 --top '$split_parms.top'
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35 --by '$split_parms.split_by.select_split_by'
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36 #if $split_parms.split_by.select_split_by == "col":
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37 --id_column '$split_parms.split_by.id_col'
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38 --match '$split_parms.split_by.match_regex'
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39 --sub '$split_parms.split_by.sub_regex'
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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40 #else
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41 --numnew '$split_parms.split_by.numnew'
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42 #if $split_parms.split_by.select_allocate.allocate == "random":
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43 --rand
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44 --seed '$split_parms.split_by.rand.seed'
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45 #end if
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46 #if $split_parms.split_by.select_allocate.allocate == "batch":
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47 --batch
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48 #end if
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49 #end if
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50 #else
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51 --numnew '$split_parms.numnew'
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52 #if $split_parms.select_allocate.allocate == "random":
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53 --rand
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54 --seed '$split_parms.select_allocate.seed'
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55 #end if
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56 #if $split_parms.select_allocate.allocate == "batch":
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57 --batch
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58 #end if
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59 #end if
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60 #if ($split_parms.select_ftype == "tabular" and $split_parms.split_by.select_split_by == "row"):
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61 --file_names '$split_parms.split_by.newfilenames'
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62 --file_ext '$split_parms.select_ftype'
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63 #end if
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64 #if $split_parms.select_ftype != "tabular":
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65 --file_names '$split_parms.newfilenames'
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66 --file_ext '$split_parms.select_ftype'
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67 #end if
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68 > '$log'
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69 ]]></command>
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70 <inputs>
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71 <conditional name="split_parms">
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72 <param name="select_ftype" type="select" label="Select the file type to split">
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73 <option value="mgf">MGF</option>
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74 <option value="fastq">FASTQ</option>
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75 <option value="tabular">Tabular</option>
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76 <option value="fasta">FASTA</option>
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77 </param>
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78 <when value="tabular">
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79 <param name="input" type="data" format="tabular" label="Tabular file to split"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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80 <param name="top" type="integer" value="0" min="0" label="Number of header lines to transfer to new files"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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81 <conditional name="split_by">
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82 <param name="select_split_by" type="select" label="Split by row or by a column?">
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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83 <option value="row">By row</option>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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84 <option value="col">By column</option>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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85 </param>
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86 <when value="col">
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87 <param name="id_col" type="data_column" label="Column to split on" data_ref="input"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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88 <param name="match_regex" type="text" label="Regex to match contents of id column" value="(.*)">
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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89 <sanitizer>
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90 <valid>
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91 <add preset="string.printable"/>
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92 <remove value="&#92;" />
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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93 <remove value="&apos;" />
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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94 </valid>
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95 <mapping initial="none">
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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96 <add source="&#92;" target="__backslash__" />
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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97 <add source="&apos;" target="__sq__"/>
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98 </mapping>
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99 </sanitizer>
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100 </param>
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101 <param name="sub_regex" type="text" label="Pattern to replace match with" value="\1">
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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102 <sanitizer>
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103 <valid>
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104 <add preset="string.printable"/>
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105 <remove value="&#92;" />
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106 <remove value="&apos;" />
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107 </valid>
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108 <mapping initial="none">
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109 <add source="&#92;" target="__backslash__" />
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110 <add source="&apos;" target="__sq__"/>
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111 </mapping>
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112 </sanitizer>
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113 </param>
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114 </when>
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115 <when value="row">
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116 <expand macro="numnew_fname"/>
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117 </when>
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118 </conditional>
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119 </when>
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120 <when value="mgf">
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121 <param name="input" type="data" format="mgf" label="MGF file to split"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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122 <expand macro="numnew_fname"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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123 </when>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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124 <when value="fastq">
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125 <param name="input" type="data" format="fastq" label="FASTQ file to split"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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126 <expand macro="numnew_fname"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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127 </when>
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128 <when value="fasta">
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129 <param name="input" type="data" format="fasta" label="FASTA file to split"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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130 <expand macro="numnew_fname"/>
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131 </when>
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132 </conditional>
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133 </inputs>
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134 <outputs>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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135 <collection name="list_output_tab" type="list" label="${tool.name} on ${on_string}: output collection">
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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136 <discover_datasets pattern="__name__" directory="out" visible="false" format="tabular"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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137 <filter>split_parms['select_ftype'] == "tabular"</filter>
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138 </collection>
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139 <collection name="list_output_mgf" type="list" label="${tool.name} on ${on_string}: output collection">
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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140 <discover_datasets pattern="__name__" directory="out" visible="false" format="mgf"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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141 <filter>split_parms['select_ftype'] == "mgf"</filter>
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142 </collection>
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143 <collection name="list_output_fasta" type="list" label="${tool.name} on ${on_string}: output collection">
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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144 <discover_datasets pattern="__name__" directory="out" visible="false" format="fasta"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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145 <filter>split_parms['select_ftype'] == "fasta"</filter>
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146 </collection>
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147 <collection name="list_output_fastq" type="list" label="${tool.name} on ${on_string}: output collection">
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148 <discover_datasets pattern="__name__" directory="out" visible="false" format="fastq"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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149 <filter>split_parms['select_ftype'] == "fastq"</filter>
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150 </collection>
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151 <data name="log" format="txt" label="${tool.name} on ${on_string}: log" />
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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152 </outputs>
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153 <tests>
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154 <test>
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155 <param name="input" value="test.tabular" ftype="tabular"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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156 <param name="select_ftype" value="tabular"/>
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157 <param name="select_split_by" value="col"/>
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158 <param name="id_col" value="1"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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159 <param name="match_regex" value="(.*)\.mgf"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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160 <param name="sub_regex" value="\1.tab"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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161 <param name="top" value="2"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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162 <output_collection name="list_output_tab" type="list">
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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163 <element name="foo.tab" file="foo.tab" ftype="tabular"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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164 <element name="foo2.tab" file="foo2.tab" ftype="tabular"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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165 <element name="foo3.tab" file="foo3.tab" ftype="tabular"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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166 </output_collection>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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167 </test>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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168 <test>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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169 <param name="input" value="test.tabular" ftype="tabular"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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170 <param name="select_ftype" value="tabular"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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171 <param name="select_split_by" value="row"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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172 <param name="top" value="2"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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173 <param name="numnew" value="2"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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174 <param name="newfilenames" value="test"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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175 <output_collection name="list_output_tab" type="list">
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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176 <element name="test_0.tabular" file="test_0.tabular" ftype="tabular"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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177 <element name="test_1.tabular" file="test_1.tabular" ftype="tabular"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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178 </output_collection>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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179 </test>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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180 <test>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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181 <param name="input" value="test.tabular" ftype="tabular"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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182 <param name="select_ftype" value="tabular"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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183 <param name="select_split_by" value="row"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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184 <param name="top" value="2"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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185 <param name="numnew" value="2"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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186 <param name="newfilenames" value="batch_tab"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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187 <param name="allocate" value="batch"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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188 <output_collection name="list_output_tab" type="list">
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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189 <element name="batch_tab_0.tabular" file="batch_tab_0.tabular" ftype="tabular"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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190 <element name="batch_tab_1.tabular" file="batch_tab_1.tabular" ftype="tabular"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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191 </output_collection>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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192 </test>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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193 <test>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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194 <param name="input" value="psm.tabular" ftype="tabular"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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195 <param name="select_ftype" value="tabular"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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196 <param name="select_split_by" value="col"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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197 <param name="id_col" value="10"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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198 <param name="match_regex" value="(.*)\.mgf"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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199 <param name="sub_regex" value="\1.tab"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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200 <param name="top" value="1"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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201 <output_collection name="list_output_tab" type="list">
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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202 <element name="file1.tab" file="file1.tab" ftype="tabular"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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203 <element name="file2.tab" file="file2.tab" ftype="tabular"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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204 <element name="file3.tab" file="file3.tab" ftype="tabular"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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205 <element name="file4.tab" file="file4.tab" ftype="tabular"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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206 </output_collection>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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207 </test>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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208 <test>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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209 <param name="input" value="demo758Dacentroid.mgf" ftype="mgf"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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210 <param name="select_ftype" value="mgf"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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211 <param name="numnew" value="3"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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212 <param name="newfilenames" value="demo"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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213 <output_collection name="list_output_mgf" type="list">
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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214 <element name="demo_0.mgf" file="demo_0.mgf" ftype="mgf"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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215 <element name="demo_1.mgf" file="demo_1.mgf" ftype="mgf"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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216 <element name="demo_2.mgf" file="demo_2.mgf" ftype="mgf"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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217 </output_collection>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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218 </test>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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219 <test>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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220 <param name="input" value="test.fasta" ftype="fasta"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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221 <param name="select_ftype" value="fasta"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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222 <param name="numnew" value="2"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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223 <param name="newfilenames" value="test"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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224 <output_collection name="list_output_fasta" type="list">
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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225 <element name="test_0.fasta" file="test_0.fasta" ftype="fasta"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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226 <element name="test_1.fasta" file="test_1.fasta" ftype="fasta"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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227 </output_collection>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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228 </test>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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229 <test>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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230 <param name="input" value="test.fastq" ftype="fastq"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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231 <param name="select_ftype" value="fastq"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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232 <param name="numnew" value="2"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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233 <param name="newfilenames" value="test"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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234 <output_collection name="list_output_fastq" type="list">
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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235 <element name="test_0.fastq" file="test_0.fastq" ftype="fastq"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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236 <element name="test_1.fastq" file="test_1.fastq" ftype="fastq"/>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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237 </output_collection>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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238 </test>
e9d56b4c3209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 85015046a6d8a9dc0f4b54611986676aceeeadd7
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239 <test>
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240 <param name="input" value="test.fasta" ftype="fasta"/>
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241 <param name="select_ftype" value="fasta"/>
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242 <param name="numnew" value="2"/>
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243 <param name="newfilenames" value="rand"/>
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244 <param name="allocate" value="random"/>
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245 <param name="seed" value="1010"/>
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246 <output_collection name="list_output_fasta" type="list">
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247 <element name="rand_0.fasta" file="rand_0.fasta" ftype="fasta"/>
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248 <element name="rand_1.fasta" file="rand_1.fasta" ftype="fasta"/>
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249 </output_collection>
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250 </test>
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251 <test>
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252 <param name="input" value="test.fasta" ftype="fasta"/>
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253 <param name="select_ftype" value="fasta"/>
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254 <param name="numnew" value="2"/>
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255 <param name="newfilenames" value="fasta_batch"/>
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256 <param name="allocate" value="batch"/>
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257 <output_collection name="list_output_fasta" type="list">
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258 <element name="fasta_batch_0.fasta" file="fasta_batch_0.fasta" ftype="fasta"/>
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259 <element name="fasta_batch_1.fasta" file="fasta_batch_1.fasta" ftype="fasta"/>
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260 </output_collection>
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261 </test>
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262 </tests>
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263 <help><![CDATA[
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264 **Split file into a dataset collection**
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265
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266 This tool can split five types of files into a separate files within a dataset collection: MGF, FASTA, FASTQ, and tabular.
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267 If a tabular file is used as input, you may choose to split by line or by column. If split by column, a new file is created for each unique value in the column.
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268 In addition, (Python) regular expressions may be used to transform the value in the column to a new value. Caution should be used with this feature, as it could transform all values to the same value, or other unexpected behavior.
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269 The default regular expression uses each value in the column without modifying it.
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270
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271 If splitting by line (or by some other item, like a FASTA entry or an MGF section), the splitting can be either done sequentially or at random.
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272 Note that there are no guarantees when splitting at random that every result file will be non-empty, so downstream tools should be able to gracefully handle empty files.
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273
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274 **Note**
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275
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276 Due to current limitations with dataset collections, a log file is produced when running this tool. It will usually be empty, but if the tool fails, any errors will be printed to the log file.
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277 ]]></help>
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278 <citations>
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279 <citation type="bibtex">
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280 @misc{githubsplit,
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281 author = {Easterly, Caleb},
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282 year = {2018},
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283 title = {split_file_to_collection: a Galaxy tool},
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284 publisher = {GitHub},
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285 journal = {GitHub repository},
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286 url = {https://github.com/galaxyproteomics/tools-galaxyp/tools/split_file_to_collection},
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287 }</citation>
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288 </citations>
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289 </tool>