Mercurial > repos > jay > pdaug_tsvtofasta

annotate PDAUG_TSVtoFASTA/PDAUG_TSVtoFASTA.xml @ 8:95c09c06f655 draft

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
author jay
date Thu, 28 Jan 2021 02:47:00 +0000
parents e9fa3b6346e3
children
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1 <tool id="pdaug_tsvtofasta" name="PDAUG TSVtoFASTA" version="0.1.0">
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3 <description>Converts tabular peptide sequence data into fasta format</description>
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5 <requirements>
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6 <requirement type="package" version="1.2.0">pandas</requirement>
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7 </requirements>
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8 <stdio>
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9 <exit_code range="1" level="fatal" />
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10 </stdio>
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11 <command detect_errors="exit_code"><![CDATA[
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12
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13 python '$__tool_directory__/PDAUG_TSVtoFASTA.py' -I '$infile' -P '$peps'
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15 #if $selmethod.method == 'withlabel'
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16 #if $selmethod.advancefeature.columnselect == 'advancefeature'
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17 --ClmPepID $selmethod.advancefeature.clmname
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18 #end if
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19 --SlcClassLabel '$selmethod.classlabel'
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20 -M '$selmethod.method'
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21 -F '$output2'
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22 -S '$output3'
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23 #end if
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25 #if $selmethod.method == 'withoutlabel'
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26 #if $selmethod.advancefeature.columnselect == 'advancefeature'
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27 --ClmPepID $selmethod.advancefeature.clmname
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28 #end if
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29 -M '$selmethod.method'
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30 -O '$output1'
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31 #end if
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33 &&
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35 ls
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37 ]]></command>
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39 <inputs>
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40 <param name="infile" type="data" label="Peptide data" format="tabular" argument= "--InFile1" help="Input tabular file"/>
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41 <param name="peps" type="text" label="Peptide Column" argument= "--PeptideColumn" help="Peptide Column Name"/>
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43 <conditional name='selmethod' >
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44 <param name="method" type="select" label="Method to convert data" argument="--Method" help="Split file if class labels are present" >
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45 <option value="withoutlabel"> Convert Without Split </option>
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46 <option value="withlabel" selected="true" >Split Data By Class Label</option>
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47 </param>
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49 <when value="withlabel">
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50 <param name="classlabel" type="text" label="Column with the class label" value="Class_label" argument= "--SlcClassLabel" help="Select Class Label"/>
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51
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52 <conditional name='advancefeature' >
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53 <param name="columnselect" type="select" label="Peptide ID Column" argument="--Method" help="Split file if class labels are present" >
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54 <option value="advancefeature" > Add Peptide ID Column Name </option>
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55 <option value="normalfeature" selected="true"> No Peptide ID Column </option>
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56 </param>
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57
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58 <when value="advancefeature">
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59 <param name="clmname" type="text" label="Column name with peptide IDs" argument= "--ClmPepID" help="Select Peptide ID Column"/>
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60 </when>
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61 <when value="normalfeature"/>
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62 </conditional>
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63 </when>
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65 <when value="withoutlabel">
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66 <conditional name='advancefeature' >
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67 <param name="columnselect" type="select" label="Column name with peptide IDs" argument="--Method" help="Split file if class labels are present" >
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68 <option value="advancefeature" > Add Peptide ID Column Name </option>
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69 <option value="normalfeature" selected="true"> No Peptide ID Column </option>
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70 </param>
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72 <when value="advancefeature">
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73 <param name="clmname" type="text" label="Select Peptide ID Column" argument= "--ClmPepID" help="Select Peptide ID Column"/>
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74 </when>
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75 <when value="normalfeature"/>
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77 </conditional>
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78 </when>
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79 </conditional>
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80 </inputs>
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82 <outputs>
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83 <data name='output1' format='fasta' label="${tool.name} on $on_string -(fasta)" >
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84 <filter>selmethod['method'] == "withoutlabel"</filter>
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85 </data>
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86
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87 <data name='output2' format='fasta' label="${tool.name} on $on_string - Second (fasta)">
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88 <filter>selmethod['method'] == "withlabel"</filter>
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89 </data>
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90
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91 <data name='output3' format='fasta' label="${tool.name} on $on_string - First (fasta)" >
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92 <filter>selmethod['method'] == "withlabel"</filter>
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93 </data>
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94 </outputs>
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95
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96 <tests>
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97
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98 <test>
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99 <param name="infile" value="test.tsv"/>
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100 <param name="method" value="withoutlabel" />
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101 <param name="peps" value="Peptides" />
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102 <output name="output1" file="out.fasta" />
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103 </test>
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104
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105 <test>
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106 <param name="infile" value="test.tsv"/>
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107 <param name="method" value="withlabel" />
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108 <param name="peps" value="Peptides" />
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109 <param name="withlabel" value="Class_label" />
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110 <output name="output2" file="1.fasta" />
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111 <output name="output3" file="2.fasta" />
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112 </test>
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113
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114 </tests>
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115 <help><![CDATA[
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116 .. class:: infomark
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117
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118 **What it does**
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119
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120 This tool converts tabular files into fasta file and split fasta file on the basis of the class label.
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121
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122 -----
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123
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124 **Inputs**
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125 * **Method to convert data** Converts tabular data into fasta with or without splitting based on the availability of class labels.
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126
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127 * **Column with the class label** Enter the column name with the class labels.
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128
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129 * **Peptide data** Enter the column name with peptides.
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130
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131 * **Peptide ID Column** Enter the column name with peptide IDs.
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132
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133 -----
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134
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135 **Outputs**
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136 * Returns fasta file.]]></help>
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137 <citations>
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138 <citation type="bibtex">
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139 @misc{PDAUGGITHUB,
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140 author = {Joshi, Jayadev and Blankenberg, Daniel},
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141 year = {2020},
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142 title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling},
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143 publisher = {GitHub},
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144 journal = {GitHub repository},
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145 url =
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146 {https://github.com/jaidevjoshi83/pdaug.git},
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147 }
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148 </citation>
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149 </citations>
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150 </tool>
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151
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152
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153