annotate clipping_profile.xml @ 63:27e16a30667a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
author iuc
date Tue, 09 Apr 2024 11:24:55 +0000
parents 473382134e56
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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 <expand macro="bio_tools"/>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11 <version_command><![CDATA[clipping_profile.py --version]]></version_command>
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12 <command><![CDATA[
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13 @BAM_SAM_INPUTS@
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14 clipping_profile.py -i 'input.${extension}' -o output -q ${mapq} -s "${layout}"
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15 ]]>
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16 </command>
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17 <inputs>
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18 <expand macro="bam_param"/>
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19 <expand macro="mapq_param"/>
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20 <expand macro="layout_param"/>
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21 <expand macro="rscript_output_param"/>
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22 </inputs>
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23 <outputs>
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24 <expand macro="pdf_output_data" filename="output.clipping_profile.pdf" label="${tool.name} on ${on_string}: PDF"/>
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25 <expand macro="xls_output_data" filename="output.clipping_profile.xls" label="${tool.name} on ${on_string}: XML"/>
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26 <expand macro="rscript_output_data" filename="output.clipping_profile.r" label="${tool.name} on ${on_string}: Rscript"/>
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27 </outputs>
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28 <tests>
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29 <test expect_num_outputs="2">
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30 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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31 <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size"/>
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32 <output name="outputxls" file="output.clipping_profile.xls" ftype="tabular"/>
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33 </test>
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34 <test expect_num_outputs="3">
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35 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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36 <param name="rscript_output" value="true"/>
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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" ftype="tabular"/>
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39 <output name="outputr" file="output.clipping_profile_r"/>
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40 </test>
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41 </tests>
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42 <help><![CDATA[
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43 clipping_profile.py
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44 +++++++++++++++++++
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46 This program is used to estimate clipping profile of RNA-seq reads from BAM or SAM file.
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47 Note that to use this funciton, CIGAR strings within SAM/BAM file should have 'S' operation
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48 (This means your reads aligner should support clipped mapping).
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50 Inputs
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51 ++++++++++++++
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53 Input BAM/SAM file
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54 Alignment file in BAM/SAM format.
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55
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56 Minimum mapping quality
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57 Minimum mapping quality for an alignment to be considered as "uniquely
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58 mapped". default=30
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60 Sequencing layout
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61 Denotes whether the sequecing was single-end (SE) or paired-end (PE).
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63 Sample Output
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64 ++++++++++++++
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66 .. image:: $PATH_TO_IMAGES/clipping_good.png
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67 :height: 600 px
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68 :width: 600 px
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69 :scale: 80 %
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71 @ABOUT@
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72
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73 ]]>
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74 </help>
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75 <expand macro="citations"/>
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76 </tool>