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1 <tool id="countmatrixforedger" name="countMatrixForEdger" version="1.0">
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2 <description>Make a count matrix for edgeR</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>
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7 <![CDATA[
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8 #for $i, $s in enumerate( $sample )#
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9 echo -e ${s.sample_data}"\t"${s.sample_name}"\t"${s.sample_group} >> script.data;
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10 #end for#
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11
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12 cat script.data > /tmp/script.data;
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13 $__tool_directory__/tools/scrsh.sh script.data;
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14
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15 cat count.matrix > $count_matrix;
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16 cat annotation > $annotation;
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17 cat script.log > $log;
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18 cat error.log > $error_log
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19
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20 ]]>
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21 </command>
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22 <inputs>
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23 <repeat name="sample" title="">
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24 <param name="sample_data" type="data" format="data" label="" help="" />
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25 <param name="sample_name" type="text" label="" help="" />
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26 <param name="sample_group" type="text" label="" help="" />
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27 </repeat>
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28 </inputs>
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29 <outputs>
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30 <!-- <data name="output" format="data" /> -->
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31 <data name="count_matrix" format="data" />
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32 <data name="annotation" format="data" />
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33 <data name="log" format="data" />
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34 <data name="error_log" format="data" />
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35 </outputs>
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36 <tests>
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37 <!-- <test>
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38 <param name="sample_0|sample_data" value="data1" />
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39 <param name="sample_1|sample_data" value="data2" />
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40 <param name="sample_2|sample_data" value="data3" />
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41 <param name="sample_3|sample_data" value="data4" />
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42 <param name="sample_0|sample_name" value="sample1" />
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43 <param name="sample_1|sample_name" value="sample2" />
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44 <param name="sample_2|sample_name" value="sample3" />
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45 <param name="sample_3|sample_name" value="sample4" />
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46 <param name="sample_0|sample_group" value="gr1" />
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47 <param name="sample_1|sample_group" value="gr1" />
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48 <param name="sample_2|sample_group" value="gr2" />
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49 <param name="sample_3|sample_group" value="gr2" />
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50 <output name="output" file="output"/>
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51
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52 </test> -->
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53 <test>
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54 <param name="sample_0|sample_data" value="data1" />
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55 <param name="sample_1|sample_data" value="data2" />
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56 <param name="sample_2|sample_data" value="data3" />
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57 <param name="sample_3|sample_data" value="data4" />
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58 <param name="sample_0|sample_name" value="sample1" />
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59 <param name="sample_1|sample_name" value="sample2" />
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60 <param name="sample_2|sample_name" value="sample3" />
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61 <param name="sample_3|sample_name" value="sample4" />
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62 <param name="sample_0|sample_group" value="gr1" />
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63 <param name="sample_1|sample_group" value="gr1" />
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64 <param name="sample_2|sample_group" value="gr2" />
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65 <param name="sample_3|sample_group" value="gr2" />
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66 <output name="count_matrix" file="count.matrix"/>
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67 <output name="annotation" file="annotation"/>
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68 <output name="log" file="script.log"/>
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69 <output name="error_log" file="error.log"/>
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70 </test>
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71
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72 </tests>
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73 <help>
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74 <![CDATA[
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75
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76 tutaj cos bedzie
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77 ]]>
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78 </help>
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79 <citations>
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80 <citation type="bibtex">
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81 @article{Berenger2014,
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82 doi = {10.1186/1758-2946-6-23},
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83 url = {http://dx.doi.org/10.1186/1758-2946-6-23},
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84 year = {2014},
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85 publisher = {Springer Nature},
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86 volume = {6},
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87 number = {1},
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88 pages = {23},
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89 author = {Francois Berenger and Arnout Voet and Xiao Lee and Kam YJ Zhang},
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90 title = {A rotation-translation invariant molecular descriptor of partial charges and its use in ligand-based virtual screening},
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91 journal = {Journal of Cheminformatics}
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92 }
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93 </citation>
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94 </citations>
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95 </tool>
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