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annotate clipping_profile.xml @ 62:473382134e56 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit ccb6f7edba5492f4750ef8a59c4f91eb67fdbbec
author iuc
date Wed, 22 Feb 2023 15:06:01 +0000
parents 5968573462fa
children 27e16a30667a
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1 <tool id="rseqc_clipping_profile" name="Clipping Profile" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_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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5 <macros>
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6 <import>rseqc_macros.xml</import>
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7 </macros>
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8
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9 <expand macro="bio_tools"/>
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10
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11 <expand macro="requirements" />
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13 <expand macro="stdio" />
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15 <version_command><![CDATA[clipping_profile.py --version]]></version_command>
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17 <command><![CDATA[
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18 @BAM_SAM_INPUTS@
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19 clipping_profile.py -i 'input.${extension}' -o output -q ${mapq} -s "${layout}"
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20 ]]>
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21 </command>
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22
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23 <inputs>
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24 <expand macro="bam_param" />
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25 <expand macro="mapq_param" />
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26 <expand macro="layout_param" />
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27 <expand macro="rscript_output_param" />
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28 </inputs>
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29
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30 <outputs>
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31 <expand macro="pdf_output_data" filename="output.clipping_profile.pdf" label="${tool.name} on ${on_string}: PDF"/>
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32 <expand macro="xls_output_data" filename="output.clipping_profile.xls" label="${tool.name} on ${on_string}: XML"/>
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33 <expand macro="rscript_output_data" filename="output.clipping_profile.r" label="${tool.name} on ${on_string}: Rscript"/>
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34 </outputs>
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36 <tests>
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37 <test>
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38 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
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39 <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size" />
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40 <output name="outputxls" file="output.clipping_profile.xls" ftype="tabular"/>
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41 </test>
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42 <test>
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43 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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44 <param name="rscript_output" value="true" />
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45 <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size" />
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46 <output name="outputxls" file="output.clipping_profile.xls" ftype="tabular"/>
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47 <output name="outputr" file="output.clipping_profile_r" />
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48 </test>
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49 </tests>
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51 <help><![CDATA[
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52 clipping_profile.py
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53 +++++++++++++++++++
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54
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55 This program is used to estimate clipping profile of RNA-seq reads from BAM or SAM file.
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56 Note that to use this funciton, CIGAR strings within SAM/BAM file should have 'S' operation
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57 (This means your reads aligner should support clipped mapping).
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58
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59 Inputs
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60 ++++++++++++++
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61
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62 Input BAM/SAM file
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63 Alignment file in BAM/SAM format.
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64
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65 Minimum mapping quality
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66 Minimum mapping quality for an alignment to be considered as "uniquely
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67 mapped". default=30
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69 Sequencing layout
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70 Denotes whether the sequecing was single-end (SE) or paired-end (PE).
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71
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72 Sample Output
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73 ++++++++++++++
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74
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75 .. image:: $PATH_TO_IMAGES/clipping_good.png
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76 :height: 600 px
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77 :width: 600 px
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78 :scale: 80 %
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79
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80 @ABOUT@
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81
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82 ]]>
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83 </help>
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85 <expand macro="citations" />
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86
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87 </tool>