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annotate sfold.xml @ 0:acd54eebaf51 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
author iuc
date Wed, 27 Nov 2024 13:22:18 +0000
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acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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1 <tool id="sfold" name="Sfold" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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2 <description>Prediction of RNA secondary structures through structure ensemble sampling</description>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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3 <macros>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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4 <import>macros.xml</import>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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5 </macros>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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6 <requirements>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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7 <expand macro="requirements"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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8 </requirements>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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9 <command detect_errors="exit_code"><![CDATA[
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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10 #if not $non_commercial_use
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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11 >&2 echo "this tool is only available for non commercial use";
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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12 exit 1;
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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13 #end if
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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14 mkdir -p 'output' &&
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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15 sfold '$fasta'
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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16 -a $a
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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17 #if $f:
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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18 -f '$f'
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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19 #end if
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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20 #if str($l) != '':
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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21 -l $l
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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22 #end if
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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23 #if $m:
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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24 -m '$m'
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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25 #end if
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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26 -w $w
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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27 -i $i
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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28 ]]></command>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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29 <inputs>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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30 <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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31 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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32 </param>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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33 <param argument="fasta" type="data" format="fasta" label="FASTA input"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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34 <param argument="-a" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Run clustering on the sampled ensemble?"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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35 <param argument="-f" type="data" format="ct" optional="true" label="Constrain data" help="Constraint syntax follows what is used in mfold 3.1"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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36 <param argument="-l" type="integer" min="0" optional="true" label="Maximum distance between paired bases"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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37 <param argument="-m" type="data" format="ct" optional="true" label="MFE structure" help="If provided, Sfold clustering module will determine the cluster to which this structure belongs."/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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38 <param argument="-w" type="integer" value="20" label="Length of antisense oligos"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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39 <param argument="-i" type="select" label="Module">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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40 <option value="0">None</option>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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41 <option value="1">Sirna</option>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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42 <option value="2">Soligo</option>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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43 <option value="3">Both</option>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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44 </param>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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45 <param name="output_selector" type="select" multiple="true" optional="true" display="checkboxes" label="Output options">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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46 <option value="ct" selected="true">Output ct files</option>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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47 <option value="bp" selected="true">Output bp files</option>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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48 <option value="clusters">Output cluster files</option>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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49 </param>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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50 </inputs>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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51 <outputs>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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52 <collection name="sfold_out" type="list" label="${tool.name} on ${on_string}: sfold log files">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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53 <discover_datasets pattern="(?P&lt;name&gt;.+)\.out$" format="txt" directory="output/"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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54 </collection>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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55 <collection name="sfold_bp" type="list" label="${tool.name} on ${on_string}: sfold bp files">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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56 <discover_datasets pattern="(?P&lt;name&gt;.+)\.bp$" format="txt" directory="output/"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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57 <filter>'bp' in output_selector</filter>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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58 </collection>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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59 <collection name="sfold_ct" type="list" label="${tool.name} on ${on_string}: sfold ct files">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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60 <discover_datasets pattern="(?P&lt;name&gt;.+)\.ct$" format="ct" directory="output/"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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61 <filter>'ct' in output_selector</filter>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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62 </collection>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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63 <collection name="sfold_cluster_out" type="list" label="${tool.name} on ${on_string}: sfold cluster log files">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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64 <discover_datasets pattern="(?P&lt;name&gt;.+)\.out$" format="txt" directory="output/clusters"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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65 <discover_datasets pattern="(?P&lt;name&gt;.+)\.list$" format="txt" directory="output/clusters"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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66 <filter>'clusters' in output_selector</filter>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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67 </collection>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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68 <collection name="sfold_cluster_bp" type="list" label="${tool.name} on ${on_string}: sfold cluster bp files">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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69 <discover_datasets pattern="(?P&lt;name&gt;.+)\.bp$" format="txt" directory="output/clusters"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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70 <filter>'clusters' in output_selector and 'bp' in output_selector</filter>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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71 </collection>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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72 <collection name="sfold_cluster_ct" type="list" label="${tool.name} on ${on_string}: sfold cluster ct files">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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73 <discover_datasets pattern="(?P&lt;name&gt;.+)\.ct$" format="ct" directory="output/clusters"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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74 <filter>'clusters' in output_selector and 'ct' in output_selector</filter>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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75 </collection>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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76 </outputs>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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77 <tests>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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78 <test expect_num_outputs="6">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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79 <param name="non_commercial_use" value="true"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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80 <param name="fasta" value="seq.fasta"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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81 <param name="a" value="true"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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82 <param name="f" value="cons.ct"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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83 <param name="l" value="30"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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84 <param name="m" value="mfe.ct"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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85 <param name="w" value="20"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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86 <param name="i" value="1"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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87 <param name="output_selector" value="ct,bp,clusters"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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88 <output_collection name="sfold_out" type="list">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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89 <element name="10structure">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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90 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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91 <has_n_lines n="770"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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parents:
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92 <has_text text="Structure 1 -28.90 0.74863E-01"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
93 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
94 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
95 <element name="10structure_2">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
96 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
97 <has_n_lines n="10"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
98 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
99 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
100 <element name="bp.dist.from.ecentroid">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
101 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
102 <has_n_lines n="1001"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
103 <has_text text="1 5"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
104 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
105 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
106 <element name="bp">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
107 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
108 <has_text text="Structure 1"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
109 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
110 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
111 <element name="bprob">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
112 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
113 <has_n_lines n="4"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
114 <has_text text=".16225072123690604808E+01L"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
115 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
116 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
117 <element name="cdf">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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118 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
119 <has_n_lines n="101"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
120 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
121 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
122 <element name="fe">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
123 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
124 <has_n_lines n="1000"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
125 <has_text text="1 -28.70"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
126 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
127 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
128 <element name="fe_init">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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129 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
130 <has_n_lines n="1002"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
131 <has_text text="Ensemble free energy (based on initial energies):-RT ln(U)= -28.297589224477537 "/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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132 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
133 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
134 <element name="loopr">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
135 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
136 <has_n_lines n="76"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
137 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
138 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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139 <element name="pdf">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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140 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
141 <has_n_lines n="21"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
142 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
143 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
144 <element name="sample">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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145 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
146 <has_n_lines n="1"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
147 <has_text text="Structure data in BP format removed to"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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148 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
149 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
150 <element name="sample_1000">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
151 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
152 <has_text text="(i j k): helix formed by base pairs i-j, (i+1)-(j-1),...,(i+k-1)-(j-k+1)"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
153 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
154 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
155 <element name="sclass">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
156 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
157 <has_text text="Sequence length = 76"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
158 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
159 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
160 <element name="sfold">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
161 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
162 <has_n_lines n="42"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
163 <has_text text="1 G"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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164 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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165 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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166 <element name="smfe">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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167 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
168 <has_n_lines n="2"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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169 <has_text text="Minimum free energy in the sample (SMFE)= -28.90 kcal/mol"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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170 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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171 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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172 <element name="sstrand">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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173 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
174 <has_n_lines n="76"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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175 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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176 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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177 </output_collection>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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178 <output_collection name="sfold_bp" type="list">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
179 <element name="ecentroid">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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180 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
181 <has_text text="1 72"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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182 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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183 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
184 </output_collection>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
185 <output_collection name="sfold_ct" type="list">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
186 <element name="ecentroid">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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187 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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188 <has_n_lines n="78"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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189 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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190 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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191 </output_collection>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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192 <output_collection name="sfold_cluster_out" type="list">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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193 <element name="c01.2dhist">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
194 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
195 <has_text text="1"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
196 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
197 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
198 <element name="c01.bp.dist.from.ccentroid">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
199 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
200 <has_text text="1"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
201 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
202 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
203 <element name="c01.bp">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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204 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
205 <has_text text="Structure 1"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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206 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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207 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
208 <element name="c01.fe">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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209 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
210 <has_text text=" 1"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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211 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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diff changeset
212 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
213 <element name="c02.2dhist">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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214 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
215 <has_text text="72"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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216 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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217 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
218 <element name="c02.bp.dist.from.ccentroid">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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219 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
220 <has_text text="1"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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221 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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222 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
223 <element name="c02.bp">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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224 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
225 <has_text text="Structure 1"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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226 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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227 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
228 <element name="c02.fe">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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229 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
230 <has_text text="10"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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231 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
232 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
233 <element name="ch.index">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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234 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
235 <has_n_lines n="19"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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236 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
237 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
238 </output_collection>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
239 <output_collection name="sfold_cluster_bp" type="list">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
240 <element name="c01.ccentroid">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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diff changeset
241 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
242 <has_text text="1 72"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
243 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
244 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
245 <element name="c02.ccentroid">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
246 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
247 <has_text text="Structure 1"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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248 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
249 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
250 </output_collection>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
251 <output_collection name="sfold_cluster_ct" type="list">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
252 <element name="c01.ccentroid">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
253 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
254 <has_n_lines n="78"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
255 <has_text text="Length: 76"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
256 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
257 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
258 <element name="c02.ccentroid">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
259 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
260 <has_n_lines n="78"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
261 <has_text text="Length: 76"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
262 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
263 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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264 </output_collection>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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265 </test>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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266 <test expect_num_outputs="4">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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267 <param name="non_commercial_use" value="true"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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268 <param name="fasta" value="seq.fasta"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
269 <param name="a" value="true"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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270 <param name="f" value="cons.ct"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
271 <param name="l" value="30"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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272 <param name="m" value="mfe.ct"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
273 <param name="w" value="20"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
274 <param name="i" value="1"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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275 <param name="output_selector" value="bp,clusters"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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276 <output_collection name="sfold_cluster_bp" type="list">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
277 <element name="c01.ccentroid">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
278 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
279 <has_text text="1 72"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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280 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
281 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
282 <element name="c02.ccentroid">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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283 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
284 <has_text text="Structure 1"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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285 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
286 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
287 </output_collection>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
diff changeset
288 <output_collection name="sfold_bp" type="list">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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289 <element name="ecentroid">
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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290 <assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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291 <has_text text="1 72"/>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
parents:
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292 </assert_contents>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
iuc
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293 </element>
acd54eebaf51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold commit 41456127d154f251438945210c2513601bd21ceb
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294 </output_collection>
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295 </test>
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296 </tests>
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297 <help><![CDATA[
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298 Sfold is a software package for statistical folding and rational design of nucleic acids.
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299
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300 It provides tools for predicting RNA secondary structures, designing antisense oligonucleotides, and analyzing RNA folding patterns. Sfold is widely used in academic research for studying
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301 RNA structure and function.
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302
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303 Input Format
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304
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305 -----------
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306
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307 The program requires one input file of RNA sequence in FASTA format.
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308
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309 Sfold options
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310
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311 ------------
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312
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313 The program can run based on the clustering on the sampled ensemble or not.
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314 It can also predict the secondary structure based on the constraint and MFE structure files.
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315 The sfold has two different modules:
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316
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317 * SiRNA : Target accessibility prediction and RNA duplex thermodynamics for rational siRNA design
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318 * Solig: Target accessibility prediction and rational design of antisense oligonucleotides and nucleic acid probes
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319
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320 The program can be run based on the above-mentioned modules, both of them or none of them.
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321
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322 Output Files
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323
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324 ------------
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325
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326 The Sfold program generates 4 different types of output files. sfold.out and sclass.out in your output log files, save the general messages from standard output/error from which you can know if your Sfold run was successful. Most of the other
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327 files contain a header section that defines the formats and meanings of the data in the output.
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328
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329 ------------
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330
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331 Important: The program usage is restricted to non-commercial and academic research.
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332 ]]>
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333 </help>
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334 <expand macro="citations" />
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335 </tool>