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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
author bgruening
date Fri, 25 May 2018 17:50:43 -0400
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children 30b199ed897d
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1 <tool id="hicup_truncater" name="Hicup Truncater" version="@VERSION@.0">
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2 <description>terminates sequence reads at specified Hi-C ligation junctions.</description>
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3 <macros>
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4 <import>hicup_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements_hicup" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 ##Dealing with fastq and fastq.gz
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9 #if $input_first_sequence.is_of_type("fastq.gz", "fastqsanger.gz"):
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10 ln -s $input_first_sequence dataset1.gz &&
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11 #set input1='dataset1.gz'
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12 #else
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13 ln -s $input_first_sequence dataset1 &&
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14 #set input1='dataset1'
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15 #end if
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16
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17 #if $input_second_sequence.is_of_type("fastq.gz", "fastqsanger.gz"):
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18 ln -s $input_second_sequence dataset2.gz &&
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19 #set input2='dataset2.gz'
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20 #else
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21 ln -s $input_second_sequence dataset2 &&
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22 #set input2='dataset2'
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23 #end if
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24
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25 hicup_truncater --zip --re1 '$re1' $advanced_options.nofill
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26 #if $advanced_options.sequences:
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27 --sequences '$advanced_options.sequences'
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28 #end if
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29 $input1 $input2
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30 ]]></command>
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31 <inputs>
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32 <expand macro="input_files" />
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33 <expand macro="re1" />
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34 <section name="advanced_options" title="Advanced options">
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35 <expand macro="no_fill" />
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36 <param argument="--sequences" type="text" value="" label="Ligation sequence" help="Instead of specifying a restriction enzyme recognition sequence, specify the ligation sequences directly"/>
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37 </section>
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38 </inputs>
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39 <outputs>
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40 <data name="hicup_truncater_summary" format="txt" label="hicup_truncater_summary.txt" from_work_dir="hicup_truncater_summary*.txt" />
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41 <data name="dataset1_trunc" format="fastq.gz" label="Hicup Dataset1 Truncation" from_work_dir="dataset1*.trunc.fastq.gz" />
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42 <data name="dataset2_trunc" format="fastq.gz" label="Hicup Dataset2 Truncation" from_work_dir="dataset2*.trunc.fastq.gz" />
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43 <data name="dataset1_truncater_barchart" format="svg" label="Hicup Dataset1 Truncation Barchart.svg" from_work_dir="dataset1*.truncation_barchart.svg" />
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44 <data name="dataset2_truncater_barchart" format="svg" label="Hicup Dataset2 Truncation Barchart.svg" from_work_dir="dataset2*.truncation_barchart.svg" />
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45 </outputs>
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46 <tests>
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47 <test>
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48 <param name="input_first_sequence" value="dataset1.fastq" ftype="fastq"/>
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49 <param name="input_second_sequence" value="dataset2.fastq" ftype="fastq"/>
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50 <param name="re1" value="A^AGCTT"/>
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51
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52 <output name="hicup_truncater_summary" file="hicup_truncater_summary.txt" lines_diff="8"/>
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53 <output name="dataset1_trunc" file="dataset1.trunc.fastq.gz" compare="sim_size"/>
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54 <output name="dataset2_trunc" file="dataset2.trunc.fastq.gz" compare="sim_size"/>
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55 <output name="dataset1_truncater_barchart" file="dataset1.truncation_barchart.svg" ftype="svg" lines_diff="1000" />
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56 <output name="dataset2_truncater_barchart" file="dataset2.truncation_barchart.svg" ftype="svg" lines_diff="1000" />
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57 </test>
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58 </tests>
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59 <help><![CDATA[
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f413e09ae289 planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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61 For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/
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63 To get more information about the truncater visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#Truncater
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64 ]]></help>
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66 <expand macro="citation_hicup" />
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67 </tool>