Mercurial > repos > yhoogstrate > segmentation_fold

annotate utils_filter-by-energy.xml @ 17:ad0af5e19601 draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit c6608bd5256e5c54cb2e01be6c184da0d2b08a7c-dirty
author yhoogstrate
date Thu, 19 May 2016 05:59:41 -0400
parents 7e5b96d45f8d
children 3fbde4864e00
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1 <tool id="smf_utils_filter-by-energy" name="filter-by-energy" version="@VERSION@-0">
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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="2.0.0">segmentation-fold-utils</requirement>
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13 </requirements>
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14 <expand macro="stdio" />
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16 <version_command>@VERSION_COMMAND_UTILS@</version_command>
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18 <command><![CDATA[
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19 segmentation-fold-utils
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20 filter-by-energy
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21 --energy ${energy}
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22 '$dbn_input_file'
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23 '$dbn_output_file_larger_or_equal'
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24 '$dbn_output_file_smaller'
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25 ]]></command>
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27 <inputs>
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28 <param name="dbn_input_file"
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29 type="data"
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30 format="dbn,txt"
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31 label="Input DBN file"
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32 help="The 'fasta'-headers should contain the genomic position being used to find overlapping reads in the BAM file"/>
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33 <param name="energy"
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34 type="float"
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35 value="0.0"
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36 argument="--energy"
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37 label="Energy value"
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38 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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39 </inputs>
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41 <outputs>
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42 <data name="dbn_output_file_larger_or_equal"
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43 format="dbn"
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44 label="${tool.name} on ${dbn_input_file.hid}: ${dbn_input_file.name} - energy larger/equal than selected"/>
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45 <data name="dbn_output_file_smaller"
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46 format="dbn"
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47 label="${tool.name} on ${dbn_input_file.hid}: ${dbn_input_file.name} - energy smaller than selected"/>
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48 </outputs>
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49
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50 <tests>
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51 <test>
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52 <param name="dbn_input_file" value="DBNFile.test_03.in.dbn" ftype="dbn"/>
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53 <param name="energy" value='0.0'/>
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54
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55 <output name="dbn_output_file_larger_or_equal" file="DBNFile.test_03.out.l.dbn" />
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56 <output name="dbn_output_file_smaller" file="DBNFile.test_03.out.s.dbn" />
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57 </test>
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58 </tests>
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60 <help><![CDATA[
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61 Filter based on whether the entries in the DBN file are already annotated or not
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62 ]]></help>
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63
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64 <expand macro="citations" />
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65 </tool>