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annotate bedToIgv.xml @ 41:7ab85ac5f64b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"
author iuc
date Thu, 04 Nov 2021 11:36:55 +0000
parents 3e38c9b3214f
children
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3e38c9b3214f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
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1 <tool id="bedtools_bedtoigv" name="bedtools BED to IGV" version="@TOOL_VERSION@" profile="@PROFILE@">
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2 <description>create batch script for taking IGV screenshots</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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7ab85ac5f64b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"
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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 <command><![CDATA[
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10 bedToIgv
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11 -i '$input'
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12 #if $sort:
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13 -sort $sort
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14 #end if
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15 $clps
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16 $name
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17 -slop $slop
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18 -img $img
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19 > '$output'
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20 ]]></command>
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21 <inputs>
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22 <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="Create IGV batch script for this @STD_BEDTOOLS_INPUT_LABEL@ file"/>
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23 <param name="sort" type="select" label="Sort BAM file by" help="The type of BAM sorting you would like to apply to each image.">
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24 <option value="">No sorting at all (default)</option>
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25 <option value="base">base</option>
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26 <option value="position">position</option>
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27 <option value="strand">strand</option>
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28 <option value="quality">quality</option>
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29 <option value="sample">sample</option>
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30 <option value="readGroup">readGroup</option>
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31 </param>
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32 <param argument="-clps" type="boolean" truevalue="-clps" falsevalue="" label="Collapse the aligned reads prior to taking a snapshot?"/>
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33 <param argument="-name" type="boolean" truevalue="-name" falsevalue="" label="Use the name field (column 4) for each image's filename." help="Default is to use chr:start-pos."/>
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34 <param argument="-slop" type="integer" min="0" value="0" label="Number of flanking base pairs on the left and right of the image."/>
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35 <param argument="-img" type="select" label="Select the type of image to be created.">
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36 <option value="png">PNG</option>
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37 <option value="eps">EPS</option>
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38 <option value="svg">SVG</option>
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39 </param>
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40 </inputs>
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41 <outputs>
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42 <data name="output" format="txt" metadata_source="input" label="BED to IGV on ${input.name}"/>
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43 </outputs>
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44 <tests>
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45 <test>
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46 <param name="input" value="bed12.bed" ftype="bed" />
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47 <output name="output" file="igv_bed_script.txt" ftype="txt" />
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48 </test>
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49 </tests>
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50 <help><![CDATA[
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51 **What it does**
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52
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53 Creates a batch script to create IGV images at each interval defined in a @STD_BEDTOOLS_INPUT_LABEL@ file.
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54
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55 **Notes**
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56
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57 (1) The resulting script is meant to be run from within IGV.
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58 (2) It is assumed that prior to running the script, you've loaded the proper genome and tracks.
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59
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60 @REFERENCES@
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61 ]]></help>
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62 <expand macro="citations" />
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63 </tool>