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1 <tool id="teste_out" name="teste_out" version="0.01">
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2 <description>teste_tools_lucas</description>
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3
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4 <command interpreter="python">
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5
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6 teste_out.py --script_path "$runMe" --interpreter "python"
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7 --tool_name "teste_out"
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8
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9
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10 --input_formats None
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11 #for intab in $input1:
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12 --input_tab "${intab},${intab.name}"
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13 #end for
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14
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15 --output_dir "./" --output_tab "$output1"
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16
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17 </command>
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18 <inputs>
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19 <param name="input_tab" multiple="true" type="data" format="None" label="Select one or more None input files from your history"
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20 help="Multiple inputs may be selected assuming the script can deal with them..."/>
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21 <param name="job_name" type="text" size="60" label="Supply a name for the outputs to remind you what they contain" value="teste_out"/>
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22
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23
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24 </inputs>
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25 <outputs>
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26 <data format="txt" name="output1" label="${job_name}"/>
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27
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28 </outputs>
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29 <configfiles>
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30 <configfile name="runMe">
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31 import sys
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32 import os
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33 import argparse
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34
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35 argp=argparse.ArgumentParser()
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36 argp.add_argument('--innames',default=None)
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37 argp.add_argument('--inpaths',default=None)
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38 argp.add_argument('--outpath',default=None)
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39 argp.add_argument('--case_sensitive',default=0)
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40 argp.add_argument('--additional_parameters',default=[],action="append")
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41 argp.add_argument('otherargs', nargs=argparse.REMAINDER)
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42 args = argp.parse_args()
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43
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44
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45 f= open(args.outpath,'w')
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46 if args.case_sensitive == 0:
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47 f.write('teste:\t'.join(args.innames.split(",")).upper())
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48 else:
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49 f.write('teste:\t'.join(args.innames.split(",")))
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50 f.close()
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51 </configfile>
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52 </configfiles>
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53 <tests>
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54
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55 <test>
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56 <param name="input_tab" value="dataset_20.dat,dataset_22.dat" />
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57 <param name="job_name" value="test1"/>
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58 <param name="runMe" value="$runMe"/>
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59 <output name="output1="teste_out_test1_output.xls" ftype="tabular"/>
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60
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61 </test>
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62
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63 </tests>
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64 <help>
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65
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66
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67 **What it Does**
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68 teste
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69
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70 **Script**
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71 Pressing execute will run the following code over your input file and generate some outputs in your history::
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72
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73
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74 import sys
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75 import os
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76 import argparse
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77
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78 argp=argparse.ArgumentParser()
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79 argp.add_argument('--innames',default=None)
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80 argp.add_argument('--inpaths',default=None)
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81 argp.add_argument('--outpath',default=None)
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82 argp.add_argument('--case_sensitive',default=0)
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83 argp.add_argument('--additional_parameters',default=[],action="append")
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84 argp.add_argument('otherargs', nargs=argparse.REMAINDER)
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85 args = argp.parse_args()
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86
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87
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88 f= open(args.outpath,'w')
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89 if args.case_sensitive == 0:
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90 f.write('teste:\t'.join(args.innames.split(",")).upper())
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91 else:
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92 f.write('teste:\t'.join(args.innames.split(",")))
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93 f.close()
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94
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95 **Attribution**
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96 This Galaxy tool was created by bioinfolucas@gmail.com at 12/03/2015 17:34:22
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97 using the Galaxy Tool Factory.
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98
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99 See https://bitbucket.org/fubar/galaxytoolfactory for details of that project
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100 Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team.
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101 Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573
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102
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103
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104 This tool was autogenerated from a user provided script using the Galaxy Tool Factory 2
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105 https://toolshed.g2.bx.psu.edu/view/fubar/tool_factory_2
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106 </help>
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107 <citations>
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108
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109 <citation type="doi">10.1093/bioinformatics/bts573</citation>
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110 </citations>
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111 </tool>
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