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1 <tool id="tagdust_paired_runner_2_31" name="Tagdust paired end runner" version="0.2">
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2 <description>Runs tagdust in paired 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"></expand>
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7 <expand macro="stdio"></expand>
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8 <expand macro="version_command"></expand>
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9 <command >
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10 @cat-archiecture@
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11 cp $read1_file read1.fastq ;
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12 cp $read2_file read2.fastq ;
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13 @tagdust-call-minus-files@
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14 read1.fastq read2.fastq ;
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15 @ls_and_barcode@
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16 </command>
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17 <inputs>
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18 <param name="read1_file" type="data" format="fastq,fastqsanger" label="Read 1 Fastq file to process" />
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19 <param name="read2_file" type="data" format="fastq,fastqsanger" label="Read 2 Fastq file to process" />
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20 <expand macro="reference_source"/>
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21 <expand macro="architecture"/>
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22 <expand macro="include_barcode_file"/>
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23 <expand macro="architecture"></expand>
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24 </inputs>
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25 <outputs>
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26 <data format="txt" name="logfile" label="Tagdust log on ${on_string}." from_work_dir="output/data_logfile.txt"/>
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27 <data format_source="read1_file" name="extracted1" label="Tagdust extracted Read1 from ${on_string}." from_work_dir="output/data_READ1.fq"/>
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28 <data format_source="read1_file" name="unextracted1" label="Tagdust un-extracted Read1 from ${on_string}." from_work_dir="output/data_un_READ1.fq"/>
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29 <data format_source="read2_file" name="extracted2" label="Tagdust extracted Read2 from ${on_string}." from_work_dir="output/data_READ2.fq"/>
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30 <data format_source="read2_file" name="unextracted2" label="Tagdust un-extracted Read2 from ${on_string}." from_work_dir="output/data_un_READ2.fq"/>
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31 <expand macro="output_barcode"/>
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32 </outputs>
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33 <tests>
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34 <!-- Large dataset in github but not toolshed -->
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35 <test>
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36 <param name="read1_file" value="C75_S29_R1_001_extracted.fastq" ftype="fastq" />
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37 <param name="read2_file" value="C75_S29_R2_001_extracted.fastq" ftype="fastq" />
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38 <param name="architecture" value="R:N" />
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39 <param name="reference_source|reference_source_selector" value="history"/>
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40 <param name="reference_source|ref_file" value="ercc_and_TPA_mouse_rRNA.fa" ftype="fasta"/>
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41 <output name="logfile" >
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42 <assert_contents>
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43 <has_text text="Determining threshold for read0." />
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44 </assert_contents>
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45 </output>
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46 <output name="extracted1" file="C75_S29__READ1.fq" compare="sim_size" delta="10000"/>
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47 <output name="unextracted1" file="C75_S29__un_READ1.fq" compare="sim_size" delta="10000"/>
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48 <output name="extracted2" file="C75_S29__READ2.fq" compare="sim_size" delta="10000"/>
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49 <output name="unextracted2" file="C75_S29__un_READ2.fq" compare="sim_size" delta="10000"/>
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50 </test>
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51 <test>
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52 <param name="read1_file" value="read1_extracted.fastq" ftype="fastqsanger" />
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53 <param name="read2_file" value="read2_extracted.fastq" ftype="fastqsanger" />
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54 <param name="architecture" value="test_R:N" />
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55 <param name="reference_source|reference_source_selector" value="history"/>
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56 <param name="reference_source|ref_file" value="ercc_and_TPA_mouse_rRNA.fa" ftype="fasta"/>
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57 <output name="logfile" >
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58 <assert_contents>
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59 <has_text text="Determining threshold for read0." />
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60 </assert_contents>
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61 </output>
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62 <output name="extracted1" file="paired_READ1.fq" ftype="fastqsanger" compare="sim_size" delta="1000"/>
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63 <output name="unextracted1" file="paired_un_READ1.fq" ftype="fastqsanger" compare="sim_size" delta="1000"/>
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64 <output name="extracted2" file="paired_READ2.fq" ftype="fastqsanger" compare="sim_size" delta="1000"/>
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65 <output name="unextracted2" file="paired_un_READ2.fq" ftype="fastqsanger" compare="sim_size" delta="1000"/>
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66 </test>
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67 <test>
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68 <param name="read1_file" value="read1_extracted.fastq" ftype="fastq" />
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69 <param name="read2_file" value="read2_extracted.fastq" ftype="fastq" />
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70 <param name="architecture" value="test_R:N" />
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71 <param name="reference_source|reference_source_selector" value="cached"/>
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72 <param name="ref_path" value="test_ercc_and_TPA_mouse_RNA"/>
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73 <output name="logfile" >
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74 <assert_contents>
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75 <has_text text="Determining threshold for read0." />
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76 </assert_contents>
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77 </output>
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78 <output name="extracted1" file="paired_READ1.fq" compare="sim_size" delta="1000"/>
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79 <output name="unextracted1" file="paired_un_READ1.fq" compare="sim_size" delta="1000"/>
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80 <output name="extracted2" file="paired_READ2.fq" compare="sim_size" delta="1000"/>
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81 <output name="unextracted2" file="paired_un_READ2.fq" compare="sim_size" delta="1000"/>
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82 </test>
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83 </tests>
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84 <help>
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85 <![CDATA[
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86 This tool runs Tagdust2 in paired end mode.
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87
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88 ]]>
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89 @tool-documentation@
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90
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91 @tagdust-documentation@
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92
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93 </help>
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94 <expand macro="citations"></expand>
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95 </tool>
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