Mercurial > repos > iuc > raceid_filtnormconf

annotate macros_inspecttrajectories.xml @ 1:01290f30211f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 71e6b205841c83391ea8fc69e10eac03f212f4d6
author iuc
date Thu, 28 Feb 2019 13:00:24 -0500
parents 8dc8ff057b0f
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8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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1 <macros>
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2 <macro name="inspecttrajectories_inputs" >
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3 <param name="inputrds" type="data" format="rdata" label="Input RDS" help="Requires the RDS output from the trajectory analysis" />
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4 <section name="trjsid" title="StemID Branch Link Examine" expanded="true" help="StemID derives cell lineage trees and predicts multipotent cell identities">
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5 <conditional name="basic" >
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6 <param name="doit" type="select" label="Perform StemID?" >
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7 <expand macro="yesno_checkedno" />
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8 </param>
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9 <when value="no" />
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10 <when value="yes" >
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11 <param name="i" type="integer" min="1" value="1" label="Cluster Number" />
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12 <param name="br" type="text" label="Trajectory Path i, j, k" help="A path of three clusters starting at i, passing through j, and ending at k." >
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13 <expand macro="sanitize_numeric_vector" />
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14 </param>
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15 <expand macro="use_defaults_no">
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16 <param name="zscore" type="boolean" checked="false" label="Plot Z-score Transformed Projections" />
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17 <param name="ndiffgenes" type="integer" min="1" value="10" label="Number of DE Genes" help="Number of differentially expressed genes to output per cluster" />
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18 </expand>
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19 </when>
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20 </conditional>
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21 </section>
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22 <section name="trjfid" title="FateID Branch Link Examine" expanded="true" help="FateID infers cell fate bias in multipotent progenitor cells" >
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23 <conditional name="basic" >
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24 <param name="doit" type="select" label="Perform FateID?" >
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25 <expand macro="yesno_checkedno" />
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26 </param>
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27 <when value="no" />
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28 <when value="yes" >
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29 <param name="cellsfromz" type="text" value="" label="Cells from Clusters" help="Vector of valid cluster numbers ordered along the trajectory" >
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30 <expand macro="sanitize_numeric_vector" />
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31 </param>
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32 <expand macro="use_defaults_no">
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33 <param name="filterset_minexpr" type="integer" min="0" value="2" label="Min Expression" help="Minimum expression required for at least minnumber cells" />
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34 <param name="filterset_minnumber" type="integer" min="0" value="1" label="Min Number of Cells" help="Minimum number of cells in which a gene needs to be expressed at least a level of minexpr."/>
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35 <param name="getsom_nb" type="integer" min="1" value="1000" label="SOM Nodes" help="Number of nodes of the self-organizing map." />
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36 <param name="getsom_alpha" type="float" min="0" value="0.5" label="Smoothing parameter" help="Pseudo-temporal expression profiles are derived by a local regression of expression values across the ordered cells using the function 'loess' from the package 'stats'. This is the parameter, which controls the degree of smoothing. Larger values return smoother profiles." />
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37 <param name="procsom_corthr" type="float" min="0" max="1" value="0.85" label="Correlation threshold" help="The z-score of the average normalized pseudo-temporal expression profiles within each node of the self-organizing map is computed, and the correlation of these z-scores between neighbouring nodes is computed. If the correlation is greater than 'corthr', neighbouring nodes are merged" />
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38 <param name="procsom_minsom" type="integer" min="0" value="3" label="Min SOM" help="Nodes of the self-organizing map with less than this number of transcripts are discarded" />
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39 <param name="plotheat_xgrid" type="boolean" checked="false" label="Partitioning along the x-axis" />
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40 <param name="plotheat_ygrid" type="boolean" checked="false" label="Partitioning along the y-axis" />
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41 <param name="plotheat_xlab" type="boolean" checked="false" label="Average position is given for each partition along the x-axis" />
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42 </expand>
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43 <conditional name="som" >
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44 <param name="doit" type="select" label="Perform Additional FateID Analysis with Self-Organised Map?" >
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45 <expand macro="yesno_checkedno" />
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46 </param>
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47 <when value="no" />
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48 <when value="yes" >
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49 <conditional name="use_genes" >
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50 <param name="typer" type="select" label="Genes to Inspect" >
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51 <option value="genelist">List of Genes</option>
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52 <option value="cln">Cluster</option>
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53 </param>
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54 <when value="genelist">
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55 <param name="use_genes" type="text" value="" label="Gene List" >
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56 <expand macro="sanitize_string_vector" />
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57 </param>
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58 </when>
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59 <when value="cln" >
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60 <param name="use_genes" type="integer" min="1" value="1" label="Cluster Number" />
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61 </when>
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62 </conditional>
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63 <param name="use_types" type="text" value="\\_\\d+" label="Types Regex (select)" help="Regex to select types across cell names" >
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64 <expand macro="sanitize_regex" />
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65 </param>
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66 <param name="title" type="text" value="Title" label="Plot title" />
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67 <expand macro="use_defaults_no">
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68 <param name="cluster" type="boolean" checked="false" label="Partitioning along the x-axis" />
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69 <param name="alpha" type="float" min="0" max="1" value="0.5" label="Smoothing parameter" />
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70 </expand>
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71 </when>
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72 </conditional>
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73 </when>
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74 </conditional>
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75 </section>
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76 </macro>
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77 <macro name="inspecttrajectories_tests" >
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78 <test>
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79 <!-- default, generates a blank report -->
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80 <param name="inputrds" value="out_traject_default.ltree.rdat" />
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81 <output name="outpdf" value="out_traject_inspect_default.ltree.blank.pdf" compare="sim_size" delta="15" />
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82 </test>
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83 <test>
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84 <!-- stemID branch inspection: vignette search "getproj" -->
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
85 <param name="inputrds" value="out_traject_default.ltree.rdat" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
86 <section name="trjsid" >
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
87 <conditional name="basic" >
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
88 <param name="doit" value="yes" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
89 <param name="i" value="3" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
90 <param name="br" value="1,3,8" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
91 </conditional>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
92 </section>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
93 <output name="outpdf" value="out_traject_inspect_stemid.pdf" compare="sim_size" delta="15" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
94 <output name="outdiffgenes" value="out_traject_inspect_stemid.tabular" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
95 </test>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
96 <test>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
97 <!-- fateID trajectory inspection: vignette search "cellsfromtree" -->
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
98 <param name="inputrds" value="out_traject_default.ltree.rdat" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
99 <section name="trjfid" >
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
100 <conditional name="basic" >
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
101 <param name="doit" value="yes" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
102 <param name="cellsfromz" value="2,1,4" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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103 <expand macro="test_nondef" >
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
104 <param name="filterset_minexpr" value="2" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
105 <param name="getsom_nb" value="1000" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
106 <param name="getsom_alpha" value="0.5" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
107 <param name="plotheat_xlab" value="true" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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108 </expand>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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109 </conditional>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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110 </section>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
111 <output name="outpdf" value="out_traject_inspect_fateid.pdf" compare="sim_size" delta="15" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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112 </test>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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113 <test>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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114 <!-- fateID trajectory inspection with som: vignette search "SOM" -->
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
115 <param name="inputrds" value="out_traject_default.ltree.rdat" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
116 <section name="trjfid" >
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
117 <conditional name="basic" >
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
118 <param name="doit" value="yes" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
119 <param name="cellsfromz" value="2,1,4" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
120 <conditional name="som" >
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
121 <param name="doit" value="yes" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
122 <expand macro="test_nondef" >
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
123 <param name="typer" value="cln" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
124 <param name="use_genes" value="12" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
125 </expand>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
126 </conditional>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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127 </conditional>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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128 </section>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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129 <output name="outpdf" value="out_traject_inspect_fateid_som.pdf" compare="sim_size" delta="15" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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130 </test>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
131 <test>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
132 <!-- uses all 3 sections with additional non-default params -->
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
133 <param name="inputrds" value="out_traject_default.ltree.rdat" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
134 <section name="trjsid" >
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
135 <conditional name="basic" >
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
136 <param name="doit" value="yes" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
137 <param name="i" value="5" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
138 <param name="br" value="6,5,3" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
139 <expand macro="test_nondef" >
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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140 <param name="zscore" value="true" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
141 <param name="ndiffgenes" value="14" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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142 </expand>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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143 </conditional>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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144 </section>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
145 <section name="trjfid" >
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
146 <conditional name="basic" >
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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147 <param name="doit" value="yes" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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148 <param name="cellsfromz" value="3,9,2" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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149 <expand macro="test_nondef" >
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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150 <param name="filterset_minexpr" value="1" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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151 <param name="filterset_minnumber" value="2" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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152 <param name="procsom_minsom" value="5" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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153 <param name="procsom_corthr" value="0.5" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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154 <param name="plotheat_ygrid" value="true" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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155 </expand>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
156 <conditional name="som" >
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
157 <param name="doit" value="yes" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
158 <conditional name="use_genes" >
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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159 <param name="typer" value="genelist" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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160 <param name="use_genes" value="Clca4,Mki67,Defa24,Ybx1,Vasp,Apoa1" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
161 <expand macro="test_nondef" >
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
162 <param name="cluster" value="true" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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163 <param name="alpha" value="0.1" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
164 </expand>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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165 </conditional>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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166 </conditional>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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167 </conditional>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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168 </section>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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169 <output name="outdiffgenes" value="out_traject_inspect_allthree.tabular" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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170 <output name="outpdf" value="out_traject_inspect_allthree.pdf" compare="sim_size" delta="15" />
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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171 </test>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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172 </macro>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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173 <token name="@INSPECTTRAJECTORIES_CHEETAH@"><![CDATA[
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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174 in.rdat = readRDS('${inputrds}')
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iuc
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175
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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176 perform.stemID = FALSE
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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177 perform.fateID = FALSE
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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178 perform.fateID.sominspect = FALSE
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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179
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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180 #if str($trjsid.basic.doit) == "yes"
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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181 perform.stemID = TRUE
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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182 trjsid.getproj = formals(getproj)
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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183
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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184 trjsid.numdiffgenes = 10
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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185 trjsid.getproj\$i = as.integer( '$trjsid.basic.i' )
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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186 trjsid.branchcells.ijk = string2numericvector( '$trjsid.basic.br' )
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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187
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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188 #if str($trjsid.basic.use.def) == "no":
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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189
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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190 trjsid.getproj\$zscore = as.logical( '$trjsid.basic.use.zscore' )
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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191 trjsid.numdiffgenes = as.integer( '$trjsid.basic.use.ndiffgenes' )
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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192
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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193 #end if
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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194 #end if
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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195
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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196 #if str($trjfid.basic.doit) == "yes":
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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197 perform.fateID = TRUE
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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198 trjfid.cellsfrom = formals(cellsfromtree)
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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199 trjfid.filterset = formals(filterset)
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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200 trjfid.getsom = formals(getsom)
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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201 trjfid.procsom = formals(procsom)
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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202 trjfid.plotheat = list()
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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203
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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204 trjfid.cellsfrom\$z = string2numericvector( '$trjfid.basic.cellsfromz' )
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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205 #if str($trjfid.basic.use.def) == "no":
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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206
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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207 trjfid.filterset\$minexpr = as.integer( '$trjfid.basic.use.filterset_minexpr' )
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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208 trjfid.filterset\$minnumber = as.integer( '$trjfid.basic.use.filterset_minnumber' )
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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209 trjfid.getsom\$nb = as.numeric( '$trjfid.basic.use.getsom_nb' )
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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210 trjfid.getsom\$alpha = as.numeric( '$trjfid.basic.use.getsom_alpha' )
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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211 trjfid.procsom\$corthr = as.numeric( '$trjfid.basic.use.procsom_corthr' )
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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212 trjfid.procsom\$minsom = as.integer( '$trjfid.basic.use.procsom_minsom' )
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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213 trjfid.plotheat\$xgrid = as.logical( '$trjfid.basic.use.plotheat_xgrid' )
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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214 trjfid.plotheat\$ygrid = as.logical( '$trjfid.basic.use.plotheat_ygrid' )
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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215 trjfid.plotheat\$xlab = as.logical( '$trjfid.basic.use.plotheat_xlab' )
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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216 #end if
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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217
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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218 #if str($trjfid.basic.som.doit) == "yes":
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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219 perform.fateID.sominspect = TRUE
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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220
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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221 trjfidsomi = list()
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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222 #if str($trjfid.basic.som.use_genes.typer) == "genelist":
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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223 trjfidsomi.use.genes = string2textvector( '$trjfid.basic.som.use_genes.use_genes' )
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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224 #else if str($trjfid.basic.som.use_genes.typer) == "cln":
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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225 trjfidsomi.use.genes = as.integer( '$trjfid.basic.som.use_genes.use_genes' )
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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226 #end if
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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227
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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228 trjfidsomi.use.types = '$trjfid.basic.som.use_types'
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
229 trjfidsomi\$name = '$trjfid.basic.som.title'
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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230
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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diff changeset
231 #if str($trjfid.basic.som.use.def) == "no":
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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diff changeset
232 trjfidsomi\$cluster = as.logical( '$trjfid.basic.som.use.cluster' )
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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233 trjfidsomi\$alpha = as.numeric( '$trjfid.basic.som.use.alpha' )
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
234 #end if
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
235 #end if
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
236 #end if
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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237
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
238 out.pdf = '${outpdf}'
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
239 out.diffgenes = '${outdiffgenes}'
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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240
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
241 ]]>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
242 </token>
8dc8ff057b0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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243 </macros>