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annotate spring_map.xml @ 2:588b45a6d6b9 draft default tip

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"planemo upload commit fe7295ad48151648562b06d5b075a68d77747326"
author guerler
date Thu, 08 Apr 2021 18:15:52 +0000
parents 338e62ac88dd
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1 <tool id="spring_map" name="SPRING Map" license="MIT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <description>with BLAST</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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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 spring_map.py
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9 @pdb_source@
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10 -l '$list'
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11 -c '$cross'
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12 -e $evalue
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13 -o '$output'
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14 -g '$log'
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15 ]]> </command>
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16 <inputs>
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17 <expand macro="pdb_source" />
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18 <param name="list" type="data" format="tabular" label="PDB Chain Identifiers" help="List of PDB chains `PDB_CHAIN`." />
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19 <param name="cross" type="data" format="tabular" label="Cross Reference (unmapped)" help="Unmapped SPRING PDB Cross Reference as produced by SPRING Cross tool." />
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20 <param name="evalue" type="float" value="0.0" min="0.0" max="1.0" label="E-value Threshold" help="Specify an e-Value threshold to filter the alignment results" />
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21 <expand macro="logfile" />
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22 </inputs>
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23 <outputs>
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24 <data format="tabular" name="output" label="SPRING Map Cross Reference" />
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25 <data format="txt" name="log" label="SPRING Map Log">
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26 <filter>logfile</filter>
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27 </data>
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28 </outputs>
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29 <tests>
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30 <test expect_num_outputs="1">
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31 <conditional name="pdb_source">
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32 <param name="pdb_source_selector" value="history" />
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33 <param name="ffdata" value="cross/pdb.ffdata" />
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34 <param name="ffindex" value="cross/pdb.ffindex" />
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35 </conditional>
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36 <param name="list" value="map/chains.tabular" ftype="tabular" />
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37 <param name="cross" value="cross/reference.tabular" ftype="tabular" />
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38 <output name="output" file="map/mapped.reference.tabular" />
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39 </test>
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40 <test expect_num_outputs="2">
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41 <conditional name="pdb_source">
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42 <param name="pdb_source_selector" value="indexed" />
2
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43 <param name="pdb" value="pdb02_cross" />
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44 <param name="zipped" value="gz" />
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45 </conditional>
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46 <param name="list" value="map/chains.tabular" ftype="tabular" />
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47 <param name="cross" value="cross/reference.tabular" ftype="tabular" />
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48 <param name="logfile" value="true" />
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49 <output name="output" file="map/mapped.reference.tabular" />
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50 </test>
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51 <test expect_num_outputs="2">
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52 <conditional name="pdb_source">
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53 <param name="pdb_source_selector" value="indexed" />
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54 <param name="pdb" value="pdb02_cross" />
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55 <param name="zipped" value="gz" />
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56 </conditional>
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57 <param name="evalue" value="0.0001" />
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58 <param name="list" value="map/chains.tabular" ftype="tabular" />
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59 <param name="cross" value="cross/reference.tabular" ftype="tabular" />
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60 <param name="logfile" value="true" />
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61 <output name="output" file="map/mapped.reference.e0001.tabular" />
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62 </test>
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63 <test expect_num_outputs="2">
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64 <conditional name="pdb_source">
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65 <param name="pdb_source_selector" value="indexed" />
0
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66 <param name="pdb" value="pdb01_cross" />
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67 </conditional>
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68 <param name="list" value="map/chains.tabular" ftype="tabular" />
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69 <param name="cross" value="cross/reference.tabular" ftype="tabular" />
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70 <param name="logfile" value="true" />
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71 <output name="output" file="map/mapped.reference.tabular" />
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72 </test>
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73 </tests>
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74 <help><![CDATA[
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75
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76 **What it does**
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77
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78 Creates additional columns for the SPRING cross reference containing the chain identifier of the homologues from the template library.
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79
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80 ]]> </help>
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81 <expand macro="citations" />
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82 </tool>