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annotate read_GC.xml @ 60:1421603cc95b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
author iuc
date Sat, 26 Nov 2022 15:19:14 +0000
parents dbedfc5f5a3c
children 5968573462fa
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60
1421603cc95b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
iuc
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1 <tool id="rseqc_read_GC" name="Read GC" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
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2 <description>determines GC% and read count</description>
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3 <expand macro="bio_tools"/>
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4 <macros>
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5 <import>rseqc_macros.xml</import>
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6 </macros>
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7
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8 <expand macro="requirements" />
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10 <expand macro="stdio" />
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12 <version_command><![CDATA[read_GC.py --version]]></version_command>
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14 <command><![CDATA[
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1421603cc95b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
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15 @BAM_SAM_INPUTS@
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16 read_GC.py
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17 --input-file 'input.${extension}'
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18 --out-prefix output
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19 --mapq ${mapq}
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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_sam_param" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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25 <expand macro="mapq_param" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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26 <expand macro="rscript_output_param" />
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27 </inputs>
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28
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29 <outputs>
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30 <expand macro="pdf_output_data" filename="output.GC_plot.pdf" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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31 <expand macro="xls_output_data" filename="output.GC.xls" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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32 <expand macro="rscript_output_data" filename="output.GC_plot.r" />
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33 </outputs>
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35 <tests>
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36 <test>
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37 <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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38 <param name="rscript_output" value="true" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
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39 <output name="outputxls" file="output.GC.xls" />
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40 <output name="outputr" file="output.GC_plot_r" />
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09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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41 <output name="outputpdf" file="output.GC_plot.pdf" compare="sim_size" />
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42 </test>
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43 </tests>
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45 <help><![CDATA[
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46 read_GC.py
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47 ++++++++++
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50 Inputs
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51 ++++++++++++++
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52
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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 Output
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57 ++++++++++++++
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58
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59 1. output.GC.xls: Two column, plain text file, first column is GC%, second column is read count
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60 2. output.GC_plot.r: R script to generate pdf file.
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61 3. output.GC_plot.pdf: graphical output generated from R script.
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62
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63 .. image:: $PATH_TO_IMAGES/read_gc.png
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64 :height: 600 px
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65 :width: 600 px
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66 :scale: 80 %
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67
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68 @ABOUT@
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69
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70 ]]>
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71 </help>
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72
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73 <expand macro="citations" />
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74
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75 </tool>