annotate macros_inspecttrajectories.xml @ 1:30d9118a650a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 71e6b205841c83391ea8fc69e10eac03f212f4d6
author iuc
date Thu, 28 Feb 2019 12:59:30 -0500
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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" -->
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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85 <param name="inputrds" value="out_traject_default.ltree.rdat" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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diff changeset
86 <section name="trjsid" >
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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87 <conditional name="basic" >
ff7cd3c7c1df 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" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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diff changeset
89 <param name="i" value="3" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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90 <param name="br" value="1,3,8" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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91 </conditional>
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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92 </section>
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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diff changeset
93 <output name="outpdf" value="out_traject_inspect_stemid.pdf" compare="sim_size" delta="15" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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94 <output name="outdiffgenes" value="out_traject_inspect_stemid.tabular" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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95 </test>
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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96 <test>
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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97 <!-- fateID trajectory inspection: vignette search "cellsfromtree" -->
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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98 <param name="inputrds" value="out_traject_default.ltree.rdat" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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99 <section name="trjfid" >
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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100 <conditional name="basic" >
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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101 <param name="doit" value="yes" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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102 <param name="cellsfromz" value="2,1,4" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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103 <expand macro="test_nondef" >
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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104 <param name="filterset_minexpr" value="2" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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105 <param name="getsom_nb" value="1000" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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106 <param name="getsom_alpha" value="0.5" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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107 <param name="plotheat_xlab" value="true" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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108 </expand>
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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109 </conditional>
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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110 </section>
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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111 <output name="outpdf" value="out_traject_inspect_fateid.pdf" compare="sim_size" delta="15" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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112 </test>
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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113 <test>
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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114 <!-- fateID trajectory inspection with som: vignette search "SOM" -->
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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115 <param name="inputrds" value="out_traject_default.ltree.rdat" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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116 <section name="trjfid" >
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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117 <conditional name="basic" >
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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118 <param name="doit" value="yes" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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119 <param name="cellsfromz" value="2,1,4" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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120 <conditional name="som" >
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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121 <param name="doit" value="yes" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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122 <expand macro="test_nondef" >
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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123 <param name="typer" value="cln" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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124 <param name="use_genes" value="12" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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diff changeset
125 </expand>
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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126 </conditional>
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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127 </conditional>
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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128 </section>
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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129 <output name="outpdf" value="out_traject_inspect_fateid_som.pdf" compare="sim_size" delta="15" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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130 </test>
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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131 <test>
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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132 <!-- uses all 3 sections with additional non-default params -->
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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diff changeset
133 <param name="inputrds" value="out_traject_default.ltree.rdat" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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134 <section name="trjsid" >
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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135 <conditional name="basic" >
ff7cd3c7c1df 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" />
ff7cd3c7c1df 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" />
ff7cd3c7c1df 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" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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139 <expand macro="test_nondef" >
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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140 <param name="zscore" value="true" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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141 <param name="ndiffgenes" value="14" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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142 </expand>
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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143 </conditional>
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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144 </section>
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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145 <section name="trjfid" >
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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146 <conditional name="basic" >
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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147 <param name="doit" value="yes" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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148 <param name="cellsfromz" value="3,9,2" />
ff7cd3c7c1df 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" >
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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150 <param name="filterset_minexpr" value="1" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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151 <param name="filterset_minnumber" value="2" />
ff7cd3c7c1df 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" />
ff7cd3c7c1df 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" />
ff7cd3c7c1df 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" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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155 </expand>
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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156 <conditional name="som" >
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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157 <param name="doit" value="yes" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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158 <conditional name="use_genes" >
ff7cd3c7c1df 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" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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160 <param name="use_genes" value="Clca4,Mki67,Defa24,Ybx1,Vasp,Apoa1" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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161 <expand macro="test_nondef" >
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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162 <param name="cluster" value="true" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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163 <param name="alpha" value="0.1" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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164 </expand>
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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165 </conditional>
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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166 </conditional>
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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167 </conditional>
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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168 </section>
ff7cd3c7c1df 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" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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170 <output name="outpdf" value="out_traject_inspect_allthree.pdf" compare="sim_size" delta="15" />
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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171 </test>
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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172 </macro>
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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173 <token name="@INSPECTTRAJECTORIES_CHEETAH@"><![CDATA[
ff7cd3c7c1df 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('${inputrds}')
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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175
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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176 perform.stemID = FALSE
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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177 perform.fateID = FALSE
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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178 perform.fateID.sominspect = FALSE
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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179
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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180 #if str($trjsid.basic.doit) == "yes"
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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181 perform.stemID = TRUE
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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182 trjsid.getproj = formals(getproj)
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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183
ff7cd3c7c1df 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
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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185 trjsid.getproj\$i = as.integer( '$trjsid.basic.i' )
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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186 trjsid.branchcells.ijk = string2numericvector( '$trjsid.basic.br' )
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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187
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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188 #if str($trjsid.basic.use.def) == "no":
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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189
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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190 trjsid.getproj\$zscore = as.logical( '$trjsid.basic.use.zscore' )
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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191 trjsid.numdiffgenes = as.integer( '$trjsid.basic.use.ndiffgenes' )
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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192
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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193 #end if
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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194 #end if
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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195
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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196 #if str($trjfid.basic.doit) == "yes":
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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197 perform.fateID = TRUE
ff7cd3c7c1df 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)
ff7cd3c7c1df 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)
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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200 trjfid.getsom = formals(getsom)
ff7cd3c7c1df 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)
ff7cd3c7c1df 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()
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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203
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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204 trjfid.cellsfrom\$z = string2numericvector( '$trjfid.basic.cellsfromz' )
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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205 #if str($trjfid.basic.use.def) == "no":
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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206
ff7cd3c7c1df 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( '$trjfid.basic.use.filterset_minexpr' )
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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208 trjfid.filterset\$minnumber = as.integer( '$trjfid.basic.use.filterset_minnumber' )
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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209 trjfid.getsom\$nb = as.numeric( '$trjfid.basic.use.getsom_nb' )
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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210 trjfid.getsom\$alpha = as.numeric( '$trjfid.basic.use.getsom_alpha' )
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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211 trjfid.procsom\$corthr = as.numeric( '$trjfid.basic.use.procsom_corthr' )
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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212 trjfid.procsom\$minsom = as.integer( '$trjfid.basic.use.procsom_minsom' )
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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213 trjfid.plotheat\$xgrid = as.logical( '$trjfid.basic.use.plotheat_xgrid' )
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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214 trjfid.plotheat\$ygrid = as.logical( '$trjfid.basic.use.plotheat_ygrid' )
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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215 trjfid.plotheat\$xlab = as.logical( '$trjfid.basic.use.plotheat_xlab' )
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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216 #end if
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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217
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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218 #if str($trjfid.basic.som.doit) == "yes":
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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219 perform.fateID.sominspect = TRUE
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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220
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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221 trjfidsomi = list()
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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222 #if str($trjfid.basic.som.use_genes.typer) == "genelist":
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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223 trjfidsomi.use.genes = string2textvector( '$trjfid.basic.som.use_genes.use_genes' )
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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224 #else if str($trjfid.basic.som.use_genes.typer) == "cln":
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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225 trjfidsomi.use.genes = as.integer( '$trjfid.basic.som.use_genes.use_genes' )
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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226 #end if
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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227
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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228 trjfidsomi.use.types = '$trjfid.basic.som.use_types'
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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229 trjfidsomi\$name = '$trjfid.basic.som.title'
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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230
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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231 #if str($trjfid.basic.som.use.def) == "no":
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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232 trjfidsomi\$cluster = as.logical( '$trjfid.basic.som.use.cluster' )
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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233 trjfidsomi\$alpha = as.numeric( '$trjfid.basic.som.use.alpha' )
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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diff changeset
234 #end if
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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diff changeset
235 #end if
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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diff changeset
236 #end if
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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237
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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238 out.pdf = '${outpdf}'
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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239 out.diffgenes = '${outdiffgenes}'
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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240
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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241 ]]>
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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242 </token>
ff7cd3c7c1df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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243 </macros>