Mercurial > repos > yhoogstrate > segmentation_fold

annotate utils_filter-by-energy.xml @ 22:01866e0e3eae draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 3814f709ce964e99fe3cf2f979c11f8f3b87bce3-dirty
author yhoogstrate
date Wed, 25 May 2016 05:12:48 -0400
parents 3fbde4864e00
children 1c6654ab2492
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1 <tool id="smf_utils_filter-by-energy" name="filter-by-energy" version="@VERSION@-1">
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2 <description>Split entries over two files based on the estimated energy</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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8 <requirements>
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9 <requirement type="package" version="2.7.10">python</requirement>
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10 <requirement type="package" version="1.9">numpy</requirement>
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11 <requirement type="package" version="0.8.2.1">pysam</requirement>
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12 <requirement type="package" version="0.6.1">htseq</requirement>
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13 <requirement type="package" version="2.0.0">segmentation-fold-utils</requirement>
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14 </requirements>
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15 <expand macro="stdio" />
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17 <version_command>@VERSION_COMMAND_UTILS@</version_command>
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19 <command><![CDATA[
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20 segmentation-fold-utils
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21 filter-by-energy
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22 --energy ${energy}
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23 '$dbn_input_file'
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24 '$dbn_output_file_larger_or_equal'
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25 '$dbn_output_file_smaller'
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26 ]]></command>
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28 <inputs>
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29 <param name="dbn_input_file"
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30 type="data"
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31 format="dbn,txt"
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32 label="Input DBN file"
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33 help="The 'fasta'-headers should contain the genomic position being used to find overlapping reads in the BAM file"/>
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34 <param name="energy"
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35 type="float"
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36 value="0.0"
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37 argument="--energy"
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38 label="Energy value"
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39 help="Entries with transitions with energy smaller than energy (&lt; e) or without transitions will be put into DBN_OUTPUT_FILE_LARGER_OR_EQUAL and those larger or equal (&gt;= e) to DBN_OUTPUT_FILE_SMALLER" />
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40 </inputs>
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41
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42 <outputs>
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43 <data name="dbn_output_file_larger_or_equal"
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44 format="dbn"
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45 label="${tool.name} on ${dbn_input_file.hid}: ${dbn_input_file.name} - energy larger/equal than selected"/>
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46 <data name="dbn_output_file_smaller"
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47 format="dbn"
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48 label="${tool.name} on ${dbn_input_file.hid}: ${dbn_input_file.name} - energy smaller than selected"/>
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49 </outputs>
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51 <tests>
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52 <test>
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53 <param name="dbn_input_file" value="DBNFile.test_03.in.dbn" ftype="dbn"/>
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54 <param name="energy" value='0.0'/>
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56 <output name="dbn_output_file_larger_or_equal" file="DBNFile.test_03.out.l.dbn" />
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57 <output name="dbn_output_file_smaller" file="DBNFile.test_03.out.s.dbn" />
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58 </test>
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59 </tests>
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61 <help><![CDATA[
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62 Filter based on whether the entries in the DBN file are already annotated or not
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63 ]]></help>
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64
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65 <expand macro="citations" />
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66 </tool>