Mercurial > repos > iuc > raceid_inspectclusters
annotate macros_inspecttrajectories.xml @ 0:9fec5dd8fbb9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
author | iuc |
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date | Thu, 22 Nov 2018 04:45:41 -0500 |
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9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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1 <macros> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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changeset
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2 <macro name="inspecttrajectories_inputs" > |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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3 <param name="inputrds" type="data" format="rdata" label="Input RDS" help="Requires the RDS output from the trajectory analysis" /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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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"> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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5 <conditional name="basic" > |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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6 <param name="doit" type="select" label="Perform StemID?" > |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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7 <expand macro="yesno_checkedno" /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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8 </param> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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9 <when value="no" /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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10 <when value="yes" > |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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11 <param name="i" type="integer" min="1" value="1" label="Cluster Number" /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
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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." > |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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13 <expand macro="sanitize_numeric_vector" /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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14 </param> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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15 <expand macro="use_defaults_no"> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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16 <param name="zscore" type="boolean" checked="false" label="Plot Z-score Transformed Projections" /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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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" /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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18 </expand> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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19 </when> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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20 </conditional> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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21 </section> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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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" > |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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23 <conditional name="basic" > |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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24 <param name="doit" type="select" label="Perform FateID?" > |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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25 <expand macro="yesno_checkedno" /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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26 </param> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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27 <when value="no" /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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28 <when value="yes" > |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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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" > |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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30 <expand macro="sanitize_numeric_vector" /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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31 </param> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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32 <expand macro="use_defaults_no"> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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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" /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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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."/> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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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." /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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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." /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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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" /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
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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" /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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39 <param name="plotheat_xgrid" type="boolean" checked="false" label="Partitioning along the x-axis" /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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40 <param name="plotheat_ygrid" type="boolean" checked="false" label="Partitioning along the y-axis" /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
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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" /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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42 </expand> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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changeset
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43 <conditional name="som" > |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
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44 <param name="doit" type="select" label="Perform Additional FateID Analysis with Self-Organised Map?" > |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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45 <expand macro="yesno_checkedno" /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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46 </param> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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47 <when value="no" /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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48 <when value="yes" > |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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49 <conditional name="use_genes" > |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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50 <param name="typer" type="select" label="Genes to Inspect" > |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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51 <option value="genelist">List of Genes</option> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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52 <option value="cln">Cluster</option> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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53 </param> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
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54 <when value="genelist"> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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55 <param name="use_genes" type="text" value="" label="Gene List" > |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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56 <expand macro="sanitize_string_vector" /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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57 </param> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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58 </when> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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59 <when value="cln" > |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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60 <param name="use_genes" type="integer" min="1" value="1" label="Cluster Number" /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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61 </when> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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62 </conditional> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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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" > |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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64 <expand macro="sanitize_regex" /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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65 </param> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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66 <param name="title" type="text" value="Title" label="Plot title" /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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67 <expand macro="use_defaults_no"> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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68 <param name="cluster" type="boolean" checked="false" label="Partitioning along the x-axis" /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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69 <param name="alpha" type="float" min="0" max="1" value="0.5" label="Smoothing parameter" /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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70 </expand> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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71 </when> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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72 </conditional> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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73 </when> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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74 </conditional> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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75 </section> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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76 </macro> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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77 <macro name="inspecttrajectories_tests" > |
9fec5dd8fbb9
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iuc
parents:
diff
changeset
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78 <test> |
9fec5dd8fbb9
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iuc
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changeset
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79 <!-- default, generates a blank report --> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
|
80 <param name="inputrds" value="out_traject_default.ltree.rdat" /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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changeset
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81 <output name="outpdf" value="out_traject_inspect_default.ltree.blank.pdf" compare="sim_size" delta="15" /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
|
82 </test> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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83 <test> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
|
84 <!-- stemID branch inspection: vignette search "getproj" --> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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85 <param name="inputrds" value="out_traject_default.ltree.rdat" /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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86 <section name="trjsid" > |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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87 <conditional name="basic" > |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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88 <param name="doit" value="yes" /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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changeset
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89 <param name="i" value="3" /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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changeset
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90 <param name="br" value="1,3,8" /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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91 </conditional> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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changeset
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92 </section> |
9fec5dd8fbb9
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iuc
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changeset
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93 <output name="outpdf" value="out_traject_inspect_stemid.pdf" compare="sim_size" delta="15" /> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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changeset
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94 <output name="outdiffgenes" value="out_traject_inspect_stemid.tabular" /> |
9fec5dd8fbb9
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iuc
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changeset
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95 </test> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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96 <test> |
9fec5dd8fbb9
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iuc
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97 <!-- fateID trajectory inspection: vignette search "cellsfromtree" --> |
9fec5dd8fbb9
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98 <param name="inputrds" value="out_traject_default.ltree.rdat" /> |
9fec5dd8fbb9
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99 <section name="trjfid" > |
9fec5dd8fbb9
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iuc
parents:
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100 <conditional name="basic" > |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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101 <param name="doit" value="yes" /> |
9fec5dd8fbb9
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" /> |
9fec5dd8fbb9
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iuc
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103 <expand macro="test_nondef" > |
9fec5dd8fbb9
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iuc
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104 <param name="filterset_minexpr" value="2" /> |
9fec5dd8fbb9
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" /> |
9fec5dd8fbb9
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" /> |
9fec5dd8fbb9
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" /> |
9fec5dd8fbb9
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iuc
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108 </expand> |
9fec5dd8fbb9
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iuc
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109 </conditional> |
9fec5dd8fbb9
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iuc
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110 </section> |
9fec5dd8fbb9
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111 <output name="outpdf" value="out_traject_inspect_fateid.pdf" compare="sim_size" delta="15" /> |
9fec5dd8fbb9
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iuc
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112 </test> |
9fec5dd8fbb9
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iuc
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113 <test> |
9fec5dd8fbb9
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iuc
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114 <!-- fateID trajectory inspection with som: vignette search "SOM" --> |
9fec5dd8fbb9
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115 <param name="inputrds" value="out_traject_default.ltree.rdat" /> |
9fec5dd8fbb9
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116 <section name="trjfid" > |
9fec5dd8fbb9
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iuc
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117 <conditional name="basic" > |
9fec5dd8fbb9
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118 <param name="doit" value="yes" /> |
9fec5dd8fbb9
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iuc
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119 <param name="cellsfromz" value="2,1,4" /> |
9fec5dd8fbb9
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iuc
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120 <conditional name="som" > |
9fec5dd8fbb9
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121 <param name="doit" value="yes" /> |
9fec5dd8fbb9
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iuc
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122 <expand macro="test_nondef" > |
9fec5dd8fbb9
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123 <param name="typer" value="cln" /> |
9fec5dd8fbb9
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124 <param name="use_genes" value="12" /> |
9fec5dd8fbb9
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iuc
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125 </expand> |
9fec5dd8fbb9
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iuc
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126 </conditional> |
9fec5dd8fbb9
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iuc
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127 </conditional> |
9fec5dd8fbb9
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128 </section> |
9fec5dd8fbb9
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129 <output name="outpdf" value="out_traject_inspect_fateid_som.pdf" compare="sim_size" delta="15" /> |
9fec5dd8fbb9
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130 </test> |
9fec5dd8fbb9
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131 <test> |
9fec5dd8fbb9
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132 <!-- uses all 3 sections with additional non-default params --> |
9fec5dd8fbb9
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133 <param name="inputrds" value="out_traject_default.ltree.rdat" /> |
9fec5dd8fbb9
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134 <section name="trjsid" > |
9fec5dd8fbb9
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135 <conditional name="basic" > |
9fec5dd8fbb9
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136 <param name="doit" value="yes" /> |
9fec5dd8fbb9
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137 <param name="i" value="5" /> |
9fec5dd8fbb9
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138 <param name="br" value="6,5,3" /> |
9fec5dd8fbb9
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139 <expand macro="test_nondef" > |
9fec5dd8fbb9
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140 <param name="zscore" value="true" /> |
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141 <param name="ndiffgenes" value="14" /> |
9fec5dd8fbb9
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142 </expand> |
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143 </conditional> |
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144 </section> |
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145 <section name="trjfid" > |
9fec5dd8fbb9
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146 <conditional name="basic" > |
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147 <param name="doit" value="yes" /> |
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148 <param name="cellsfromz" value="3,9,2" /> |
9fec5dd8fbb9
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149 <expand macro="test_nondef" > |
9fec5dd8fbb9
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150 <param name="filterset_minexpr" value="1" /> |
9fec5dd8fbb9
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151 <param name="filterset_minnumber" value="2" /> |
9fec5dd8fbb9
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152 <param name="procsom_minsom" value="5" /> |
9fec5dd8fbb9
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153 <param name="procsom_corthr" value="0.5" /> |
9fec5dd8fbb9
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154 <param name="plotheat_ygrid" value="true" /> |
9fec5dd8fbb9
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155 </expand> |
9fec5dd8fbb9
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156 <conditional name="som" > |
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157 <param name="doit" value="yes" /> |
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158 <conditional name="use_genes" > |
9fec5dd8fbb9
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159 <param name="typer" value="genelist" /> |
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iuc
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160 <param name="use_genes" value="Clca4,Mki67,Defa24,Ybx1,Vasp,Apoa1" /> |
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161 <expand macro="test_nondef" > |
9fec5dd8fbb9
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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> |
9fec5dd8fbb9
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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[ |
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174 in.rdat = readRDS('${inputrds}') |
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175 |
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176 perform.stemID = FALSE |
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177 perform.fateID = FALSE |
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178 perform.fateID.sominspect = FALSE |
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179 |
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180 #if str($trjsid.basic.doit) == "yes" |
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181 perform.stemID = TRUE |
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182 trjsid.getproj = formals(getproj) |
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183 |
9fec5dd8fbb9
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184 trjsid.numdiffgenes = 10 |
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185 trjsid.getproj\$i = as.integer( '$trjsid.basic.i' ) |
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186 trjsid.branchcells.ijk = string2numericvector( '$trjsid.basic.br' ) |
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187 |
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188 #if str($trjsid.basic.use.def) == "no": |
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189 |
9fec5dd8fbb9
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190 trjsid.getproj\$zscore = as.logical( '$trjsid.basic.use.zscore' ) |
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191 trjsid.numdiffgenes = as.integer( '$trjsid.basic.use.ndiffgenes' ) |
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192 |
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193 #end if |
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194 #end if |
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195 |
9fec5dd8fbb9
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196 #if str($trjfid.basic.doit) == "yes": |
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197 perform.fateID = TRUE |
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198 trjfid.cellsfrom = formals(cellsfromtree) |
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199 trjfid.filterset = formals(filterset) |
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200 trjfid.getsom = formals(getsom) |
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201 trjfid.procsom = formals(procsom) |
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202 trjfid.plotheat = list() |
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203 |
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204 trjfid.cellsfrom\$z = string2numericvector( '$trjfid.basic.cellsfromz' ) |
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205 #if str($trjfid.basic.use.def) == "no": |
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206 |
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207 trjfid.filterset\$minexpr = as.integer( '$trjfid.basic.use.filterset_minexpr' ) |
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208 trjfid.filterset\$minnumber = as.integer( '$trjfid.basic.use.filterset_minnumber' ) |
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209 trjfid.getsom\$nb = as.numeric( '$trjfid.basic.use.getsom_nb' ) |
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210 trjfid.getsom\$alpha = as.numeric( '$trjfid.basic.use.getsom_alpha' ) |
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211 trjfid.procsom\$corthr = as.numeric( '$trjfid.basic.use.procsom_corthr' ) |
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212 trjfid.procsom\$minsom = as.integer( '$trjfid.basic.use.procsom_minsom' ) |
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213 trjfid.plotheat\$xgrid = as.logical( '$trjfid.basic.use.plotheat_xgrid' ) |
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214 trjfid.plotheat\$ygrid = as.logical( '$trjfid.basic.use.plotheat_ygrid' ) |
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215 trjfid.plotheat\$xlab = as.logical( '$trjfid.basic.use.plotheat_xlab' ) |
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216 #end if |
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217 |
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218 #if str($trjfid.basic.som.doit) == "yes": |
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219 perform.fateID.sominspect = TRUE |
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220 |
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221 trjfidsomi = list() |
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222 #if str($trjfid.basic.som.use_genes.typer) == "genelist": |
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223 trjfidsomi.use.genes = string2textvector( '$trjfid.basic.som.use_genes.use_genes' ) |
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224 #else if str($trjfid.basic.som.use_genes.typer) == "cln": |
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225 trjfidsomi.use.genes = as.integer( '$trjfid.basic.som.use_genes.use_genes' ) |
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226 #end if |
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227 |
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228 trjfidsomi.use.types = '$trjfid.basic.som.use_types' |
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229 trjfidsomi\$name = '$trjfid.basic.som.title' |
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230 |
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231 #if str($trjfid.basic.som.use.def) == "no": |
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232 trjfidsomi\$cluster = as.logical( '$trjfid.basic.som.use.cluster' ) |
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233 trjfidsomi\$alpha = as.numeric( '$trjfid.basic.som.use.alpha' ) |
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234 #end if |
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235 #end if |
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236 #end if |
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237 |
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238 out.pdf = '${outpdf}' |
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239 out.diffgenes = '${outdiffgenes}' |
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240 |
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241 ]]> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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242 </token> |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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243 </macros> |