Mercurial > repos > iuc > raceid_inspecttrajectory

annotate macros_inspecttrajectories.xml @ 1:7967b3d036d1 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 12:58:58 -0500
parents e0e9b24d76aa
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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" -->
e0e9b24d76aa 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" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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86 <section name="trjsid" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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87 <conditional name="basic" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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88 <param name="doit" value="yes" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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89 <param name="i" value="3" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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90 <param name="br" value="1,3,8" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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91 </conditional>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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92 </section>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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93 <output name="outpdf" value="out_traject_inspect_stemid.pdf" compare="sim_size" delta="15" />
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94 <output name="outdiffgenes" value="out_traject_inspect_stemid.tabular" />
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95 </test>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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96 <test>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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97 <!-- fateID trajectory inspection: vignette search "cellsfromtree" -->
e0e9b24d76aa 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" />
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iuc
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99 <section name="trjfid" >
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iuc
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100 <conditional name="basic" >
e0e9b24d76aa 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" />
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iuc
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102 <param name="cellsfromz" value="2,1,4" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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103 <expand macro="test_nondef" >
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iuc
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104 <param name="filterset_minexpr" value="2" />
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iuc
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105 <param name="getsom_nb" value="1000" />
e0e9b24d76aa 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" />
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iuc
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107 <param name="plotheat_xlab" value="true" />
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108 </expand>
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109 </conditional>
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110 </section>
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111 <output name="outpdf" value="out_traject_inspect_fateid.pdf" compare="sim_size" delta="15" />
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112 </test>
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113 <test>
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iuc
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114 <!-- fateID trajectory inspection with som: vignette search "SOM" -->
e0e9b24d76aa 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" />
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116 <section name="trjfid" >
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iuc
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117 <conditional name="basic" >
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iuc
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118 <param name="doit" value="yes" />
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iuc
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119 <param name="cellsfromz" value="2,1,4" />
e0e9b24d76aa 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" >
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iuc
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121 <param name="doit" value="yes" />
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iuc
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122 <expand macro="test_nondef" >
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iuc
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123 <param name="typer" value="cln" />
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iuc
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124 <param name="use_genes" value="12" />
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125 </expand>
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iuc
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126 </conditional>
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127 </conditional>
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128 </section>
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129 <output name="outpdf" value="out_traject_inspect_fateid_som.pdf" compare="sim_size" delta="15" />
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130 </test>
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131 <test>
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132 <!-- uses all 3 sections with additional non-default params -->
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iuc
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133 <param name="inputrds" value="out_traject_default.ltree.rdat" />
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iuc
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134 <section name="trjsid" >
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iuc
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135 <conditional name="basic" >
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iuc
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136 <param name="doit" value="yes" />
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iuc
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137 <param name="i" value="5" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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138 <param name="br" value="6,5,3" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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139 <expand macro="test_nondef" >
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140 <param name="zscore" value="true" />
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141 <param name="ndiffgenes" value="14" />
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142 </expand>
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143 </conditional>
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144 </section>
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iuc
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145 <section name="trjfid" >
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iuc
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146 <conditional name="basic" >
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iuc
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147 <param name="doit" value="yes" />
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148 <param name="cellsfromz" value="3,9,2" />
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iuc
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149 <expand macro="test_nondef" >
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iuc
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150 <param name="filterset_minexpr" value="1" />
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151 <param name="filterset_minnumber" value="2" />
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152 <param name="procsom_minsom" value="5" />
e0e9b24d76aa 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" />
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154 <param name="plotheat_ygrid" value="true" />
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155 </expand>
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156 <conditional name="som" >
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iuc
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157 <param name="doit" value="yes" />
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158 <conditional name="use_genes" >
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159 <param name="typer" value="genelist" />
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160 <param name="use_genes" value="Clca4,Mki67,Defa24,Ybx1,Vasp,Apoa1" />
e0e9b24d76aa 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" >
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162 <param name="cluster" value="true" />
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163 <param name="alpha" value="0.1" />
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164 </expand>
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165 </conditional>
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166 </conditional>
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167 </conditional>
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168 </section>
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169 <output name="outdiffgenes" value="out_traject_inspect_allthree.tabular" />
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170 <output name="outpdf" value="out_traject_inspect_allthree.pdf" compare="sim_size" delta="15" />
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171 </test>
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172 </macro>
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173 <token name="@INSPECTTRAJECTORIES_CHEETAH@"><![CDATA[
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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174 in.rdat = readRDS('${inputrds}')
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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175
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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176 perform.stemID = FALSE
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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177 perform.fateID = FALSE
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178 perform.fateID.sominspect = FALSE
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179
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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180 #if str($trjsid.basic.doit) == "yes"
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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181 perform.stemID = TRUE
e0e9b24d76aa 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)
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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183
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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184 trjsid.numdiffgenes = 10
e0e9b24d76aa 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( '$trjsid.basic.i' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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186 trjsid.branchcells.ijk = string2numericvector( '$trjsid.basic.br' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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187
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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188 #if str($trjsid.basic.use.def) == "no":
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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189
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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190 trjsid.getproj\$zscore = as.logical( '$trjsid.basic.use.zscore' )
e0e9b24d76aa 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( '$trjsid.basic.use.ndiffgenes' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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192
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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193 #end if
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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194 #end if
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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195
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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196 #if str($trjfid.basic.doit) == "yes":
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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197 perform.fateID = TRUE
e0e9b24d76aa 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)
e0e9b24d76aa 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)
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200 trjfid.getsom = formals(getsom)
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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201 trjfid.procsom = formals(procsom)
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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202 trjfid.plotheat = list()
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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203
e0e9b24d76aa 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( '$trjfid.basic.cellsfromz' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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205 #if str($trjfid.basic.use.def) == "no":
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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206
e0e9b24d76aa 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( '$trjfid.basic.use.filterset_minexpr' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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208 trjfid.filterset\$minnumber = as.integer( '$trjfid.basic.use.filterset_minnumber' )
e0e9b24d76aa 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( '$trjfid.basic.use.getsom_nb' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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210 trjfid.getsom\$alpha = as.numeric( '$trjfid.basic.use.getsom_alpha' )
e0e9b24d76aa 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( '$trjfid.basic.use.procsom_corthr' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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212 trjfid.procsom\$minsom = as.integer( '$trjfid.basic.use.procsom_minsom' )
e0e9b24d76aa 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( '$trjfid.basic.use.plotheat_xgrid' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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214 trjfid.plotheat\$ygrid = as.logical( '$trjfid.basic.use.plotheat_ygrid' )
e0e9b24d76aa 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( '$trjfid.basic.use.plotheat_xlab' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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216 #end if
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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217
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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218 #if str($trjfid.basic.som.doit) == "yes":
e0e9b24d76aa 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
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220
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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221 trjfidsomi = list()
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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222 #if str($trjfid.basic.som.use_genes.typer) == "genelist":
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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223 trjfidsomi.use.genes = string2textvector( '$trjfid.basic.som.use_genes.use_genes' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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224 #else if str($trjfid.basic.som.use_genes.typer) == "cln":
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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225 trjfidsomi.use.genes = as.integer( '$trjfid.basic.som.use_genes.use_genes' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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226 #end if
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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227
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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228 trjfidsomi.use.types = '$trjfid.basic.som.use_types'
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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229 trjfidsomi\$name = '$trjfid.basic.som.title'
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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230
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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231 #if str($trjfid.basic.som.use.def) == "no":
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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232 trjfidsomi\$cluster = as.logical( '$trjfid.basic.som.use.cluster' )
e0e9b24d76aa 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( '$trjfid.basic.som.use.alpha' )
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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234 #end if
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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235 #end if
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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236 #end if
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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237
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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238 out.pdf = '${outpdf}'
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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239 out.diffgenes = '${outdiffgenes}'
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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240
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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241 ]]>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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242 </token>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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243 </macros>