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annotate clipping_profile.xml @ 59:dbedfc5f5a3c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 247059e2527b66f1dbecf1e61496daef921040c3"
author iuc
date Sat, 18 Dec 2021 19:41:19 +0000
parents 09846d5169fa
children 1421603cc95b
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dbedfc5f5a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 247059e2527b66f1dbecf1e61496daef921040c3"
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1 <tool id="rseqc_clipping_profile" name="Clipping Profile" version="@TOOL_VERSION@">
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2 <description>
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3 estimates clipping profile of RNA-seq reads from BAM or SAM file
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4 </description>
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dbedfc5f5a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 247059e2527b66f1dbecf1e61496daef921040c3"
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5 <expand macro="bio_tools"/>
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6 <macros>
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7 <import>rseqc_macros.xml</import>
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8 </macros>
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9
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10 <expand macro="requirements" />
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12 <expand macro="stdio" />
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14 <version_command><![CDATA[clipping_profile.py --version]]></version_command>
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16 <command><![CDATA[
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17 clipping_profile.py -i '${input}' -o output -q ${mapq} -s "${layout}"
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18 ]]>
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19 </command>
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20
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21 <inputs>
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22 <expand macro="bam_param" />
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23 <expand macro="mapq_param" />
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24 <expand macro="layout_param" />
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25 <expand macro="rscript_output_param" />
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26 </inputs>
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27
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28 <outputs>
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29 <expand macro="pdf_output_data" filename="output.clipping_profile.pdf" />
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30 <expand macro="xls_output_data" filename="output.clipping_profile.xls" />
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31 <expand macro="rscript_output_data" filename="output.clipping_profile.r" />
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32 </outputs>
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34 <tests>
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35 <test>
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36 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
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37 <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size" />
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38 <output name="outputxls" file="output.clipping_profile.xls" />
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39 </test>
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40 <test>
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41 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
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42 <param name="rscript_output" value="true" />
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43 <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size" />
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44 <output name="outputxls" file="output.clipping_profile.xls" />
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45 <output name="outputr" file="output.clipping_profile_r" />
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46 </test>
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47 </tests>
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49 <help><![CDATA[
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50 clipping_profile.py
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51 +++++++++++++++++++
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52
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53 This program is used to estimate clipping profile of RNA-seq reads from BAM or SAM file.
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54 Note that to use this funciton, CIGAR strings within SAM/BAM file should have 'S' operation
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55 (This means your reads aligner should support clipped mapping).
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56
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57 Inputs
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58 ++++++++++++++
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60 Input BAM/SAM file
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61 Alignment file in BAM/SAM format.
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62
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63 Minimum mapping quality
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64 Minimum mapping quality for an alignment to be considered as "uniquely
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65 mapped". default=30
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67 Sequencing layout
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68 Denotes whether the sequecing was single-end (SE) or paired-end (PE).
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69
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70 Sample Output
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71 ++++++++++++++
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72
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73 .. image:: $PATH_TO_IMAGES/clipping_good.png
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74 :height: 600 px
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75 :width: 600 px
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76 :scale: 80 %
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77
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78 @ABOUT@
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79
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80 ]]>
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81 </help>
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83 <expand macro="citations" />
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84
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85 </tool>