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annotate hicup_truncater.xml @ 0:f413e09ae289 draft

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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
author bgruening
date Thu, 09 Mar 2017 09:32:44 -0500
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f413e09ae289 planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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1 <tool id="hicup_truncater" name="Hicup Truncater" version="0.1.0">
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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 <expand macro="stdio" />
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8 <command><![CDATA[
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9 hicup_truncater --re1 '$re1' $advanced_options.nofill
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10 #if $advanced_options.sequences:
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11 --sequences '$advanced_options.sequences'
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12 #end if
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13 '$input_first_sequence' '$input_second_sequence'
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f413e09ae289 planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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15 && mv hicup_truncater_summary* hicup_truncater_summary.txt
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16 && trunc_result_1=\$(echo '$input_first_sequence' | rev | cut -d'/' -f1 | rev)
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18 && mv \$trunc_result_1.trunc.fastq dataset1.trunc.fastq
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19 && trunc_result_2=\$(echo '$input_second_sequence' | rev | cut -d'/' -f1 | rev)
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20 && mv \$trunc_result_2.trunc.fastq dataset2.trunc.fastq
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21 && mv \$trunc_result_1.truncation_barchart.svg dataset1.truncation_barchart.svg
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22 && mv \$trunc_result_2.truncation_barchart.svg dataset2.truncation_barchart.svg
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23
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24 ]]></command>
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25 <inputs>
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26 <expand macro="input_files" />
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27 <expand macro="re1" />
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28 <section name="advanced_options" title="Advanced options">
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29 <expand macro="no_fill" />
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30 <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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31 </section>
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32 </inputs>
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33 <outputs>
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34 <expand macro="truncater_output" />
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35
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="input_first_sequence" value="dataset1.fastq" ftype="fastq"/>
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40 <param name="input_second_sequence" value="dataset2.fastq" ftype="fastq"/>
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41 <param name="re1" value="A^AGCTT"/>
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42
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43 <output name="hicup_truncater_summary" file="hicup_truncater_summary.txt" lines_diff="8"/>
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44 <output name="dataset1_trunc" file="dataset1.trunc.fastq" lines_diff="8" />
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45 <output name="dataset2_trunc" file="dataset2.trunc.fastq" lines_diff="8"/>
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46 <output name="dataset1_truncater_barchart" file="dataset1.truncation_barchart.svg" ftype="svg" lines_diff="1000" />
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47 <output name="dataset2_truncater_barchart" file="dataset2.truncation_barchart.svg" ftype="svg" lines_diff="1000" />
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48 </test>
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49 </tests>
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50 <help><![CDATA[
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52 For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/
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54 To get more information about the truncater visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#Truncater
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55 ]]></help>
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57 <expand macro="citation_hicup" />
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58 </tool>