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

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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
children
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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 <macros>
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4 <import>rseqc_macros.xml</import>
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5 </macros>
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <version_command><![CDATA[read_GC.py --version]]></version_command>
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10 <command><![CDATA[
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11 @BAM_SAM_INPUTS@
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12 read_GC.py
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13 --input-file 'input.${extension}'
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14 --out-prefix output
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15 --mapq ${mapq}
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16 ]]>
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17 </command>
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18 <inputs>
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19 <expand macro="bam_sam_param"/>
27e16a30667a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
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20 <expand macro="mapq_param"/>
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21 <expand macro="rscript_output_param"/>
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22 </inputs>
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23 <outputs>
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24 <expand macro="pdf_output_data" filename="output.GC_plot.pdf" label="${tool.name} on ${on_string}: plot (PDF)"/>
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25 <expand macro="xls_output_data" filename="output.GC.xls" label="${tool.name} on ${on_string}: XLS"/>
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26 <expand macro="rscript_output_data" filename="output.GC_plot.r" label="${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="3">
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30 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
27e16a30667a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
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31 <param name="rscript_output" value="true"/>
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32 <output name="outputxls" file="output.GC.xls" ftype="tabular"/>
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33 <output name="outputr" file="output.GC_plot_r"/>
27e16a30667a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
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34 <output name="outputpdf" file="output.GC_plot.pdf" compare="sim_size"/>
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35 </test>
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36 </tests>
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37 <help><![CDATA[
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38 read_GC.py
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39 ++++++++++
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42 Inputs
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43 ++++++++++++++
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45 Input BAM/SAM file
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46 Alignment file in BAM/SAM format.
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48 Output
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49 ++++++++++++++
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51 1. output.GC.xls: Two column, plain text file, first column is GC%, second column is read count
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52 2. output.GC_plot.r: R script to generate pdf file.
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53 3. output.GC_plot.pdf: graphical output generated from R script.
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54
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55 .. image:: $PATH_TO_IMAGES/read_gc.png
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56 :height: 600 px
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57 :width: 600 px
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58 :scale: 80 %
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60 @ABOUT@
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62 ]]>
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63 </help>
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64 <expand macro="citations"/>
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65 </tool>