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1 <tool id="tagdust_single_runner_2_31" name="Tagdust single end runner" version="0.2">
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2 <description>Runs tagdust in single end mode</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command >
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10 @cat-archiecture@
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11 cp $fastq_file input.fastq ;
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12 @tagdust-call-minus-files@
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13 input.fastq ;
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14 @ls_and_barcode@
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15 </command>
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16 <inputs>
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17 <param name="fastq_file" type="data" format="fastq,fastqsanger" label="Fastq file to process" />
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18 <expand macro="reference_source"/>
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19 <expand macro="architecture"/>
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20 <expand macro="include_barcode_file"/>
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21 </inputs>
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22 <outputs>
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23 <data format="txt" name="logfile" label="Tagdust log on ${on_string} ." from_work_dir="output/data_logfile.txt"/>
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24 <data format_source="fastq_file" name="extracted" label="Tagdust extracted reads from ${on_string}." from_work_dir="output/data.fq"/>
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25 <data format_source="fastq_file" name="unextracted" label="Tagdust un-extracted reads from ${on_string}." from_work_dir="output/data_un.fq"/>
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26 <expand macro="output_barcode"/>
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27 </outputs>
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28 <tests>
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29 <!-- Large dataset in github but not toolshed -->
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30 <!--test>
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31 <param name="fastq_file" value="C75_S29_R1_001.fastq" ftype="fastq" />
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32 <param name="architecture" value="F:NNNNNNNN_S:TATAGGG_R:N" />
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33 <param name="include|barcode_files" value="no" />
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34 <output name="logfile" >
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35 <assert_contents>
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36 <has_text text="Determining threshold for read0." />
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37 </assert_contents>
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38 </output>
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39 <output name="extracted" file="C75_S29_R1_001.fq" compare="sim_size" delta="10000"/>
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40 <output name="unextracted" file="C75_S29_R1_001_un.fq" compare="sim_size" delta="10000"/>
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41 </test-->
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42 <test>
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43 <param name="fastq_file" value="read1.fastq" ftype="fastqsanger" />
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44 <param name="architecture" value="test_F:NNNNNNNN_S:TATAGGG_R:N" />
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45 <param name="barcode_files" value="no" />
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46 <output name="logfile" >
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47 <assert_contents>
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48 <has_text text="Determining threshold for read0." />
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49 </assert_contents>
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50 </output>
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51 <output name="extracted" file="read1.fq" ftype="fastqsanger" compare="sim_size" delta="1000"/>
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52 <output name="unextracted" file="read1_un.fq" ftype="fastqsanger" compare="sim_size" delta="1000"/>
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53 </test>
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54 <test>
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55 <param name="run_type_selector" value="single"/>
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56 <param name="fastq_file" value="read1.fastq" ftype="fastq" />
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57 <param name="architecture" value="test_B:GTA_AAC_R:N" />
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58 <param name="include|barcode_files" value="yes" />
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59 <output name="logfile" >
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60 <assert_contents>
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61 <has_text text="Determining threshold for read0." />
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62 </assert_contents>
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63 </output>
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64 <output name="extracted" file="with_b_.fq"/>
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65 <output name="unextracted" file="with_b_un.fq"/>
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66 <output name="barcode_files">
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67 <assert_contents>
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68 <has_line line="data_BC_AAC.fq" />
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69 <has_line line="data_BC_GTA.fq" />
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70 </assert_contents>
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71 <discovered_dataset designation="AAC" ftype="fastq" file="with_b_BC_AAC.fq"/>
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72 <discovered_dataset designation="GTA" ftype="fastq" file="with_b_BC_GTA.fq"/>
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73 </output>
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74 </test>
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75 </tests>
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76 <help>
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77 <![CDATA[
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78 This tool runs Tagdust2 in single mode.
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79
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80 ]]>
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81 @tool-documentation@
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82
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83 @tagdust-documentation@
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84
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85 </help>
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86 <expand macro="citations"></expand>
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87 </tool>
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