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annotate gc_skew.xml @ 13:8b1cf140bbd4 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 0cfd88d16b0b20a66d4b21b037ddee6a8c440d88
author iuc
date Wed, 12 Apr 2023 15:08:23 +0000
parents 0ee66defe58b
children
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1 <?xml version="1.0"?>
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2 <tool id="circos_gc_skew" name="GC Skew" version="@WRAPPER_VERSION@">
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3 <description>calculates skew over genomic sequences</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
9
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7 <edam_topics>
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8 <edam_topic>topic_0797</edam_topic>
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9 <edam_topic>topic_0092</edam_topic>
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10 </edam_topics>
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11 <edam_operations>
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12 <edam_operation>operation_0262</edam_operation>
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13 </edam_operations>
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14 <expand macro="requirements">
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15 </expand>
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16 <command detect_errors="exit_code"><![CDATA[
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17 ln -s -f
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18 #if $reference_genome.reference_genome_source == "history"
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19 '$reference_genome.history_item'
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20 #else
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21 '$reference_genome.builtin.fields.path'
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22 #end if
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23 reference.fa &&
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24
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25 python '$__tool_directory__/gc_skew.py' reference.fa '$window' '$output'
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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26 ]]></command>
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27 <inputs>
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28 <conditional name="reference_genome">
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29 <param label="Source for reference genome" name="reference_genome_source" type="select">
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30 <option selected="True" value="history">Use a genome from history</option>
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31 <option value="builtin">Use a built-in genome"</option>
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32 </param>
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33 <when value="history">
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34 <param format="fasta" type="data" name="history_item" label="Select a reference genome"/>
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35 </when>
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36 <when value="builtin">
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37 <param label="Select a reference genome" name="builtin" type="select">
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38 <options from_data_table="all_fasta">
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39 <filter column="2" type="sort_by" />
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40 <validator message="No genomes are available for the selected input dataset" type="no_options" />
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41 </options>
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42 </param>
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43 </when>
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44 </conditional>
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45 <param argument="window" type="integer" min="1" value="100000" label="Window size" />
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46 </inputs>
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47 <outputs>
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48 <data name="output" format="bigwig" />
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49 </outputs>
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50 <tests>
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51 <test>
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52 <conditional name="reference_genome">
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53 <param name="reference_genome_source" value="history" />
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54 <param name="history_item" value="gc_skew/1.fa" ftype="fasta"/>
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55 </conditional>
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56 <param name="window" value="2" />
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57 <output name="output" file="gc_skew/1.bw" ftype="bigwig" />
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58 </test>
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59 </tests>
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60 <help><![CDATA[
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61 Calculate GC skew (G-C)/(G+C) for multiple windows along the sequence.
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62
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63 Returns a list of ratios (floats), controlled by the length of the sequence and the size of the window.
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64
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65 Returns 0 for windows without any G/C by handling zero division errors.
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66
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67 Does NOT look at any ambiguous nucleotides.
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68 ]]></help>
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69 <expand macro="citations" />
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70 </tool>