Mercurial > repos > iuc > raceid_clustering
comparison raceid_clustering.xml @ 8:f911a64454fb draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 455bad7eca54164f95755174904842907846bb42"
author | iuc |
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date | Mon, 20 Dec 2021 10:12:47 +0000 |
parents | c4f39bf4a068 |
children | 0bff0ee0683a |
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7:c4f39bf4a068 | 8:f911a64454fb |
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1 <tool id="raceid_clustering" name="Clustering using RaceID" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" > | 1 <tool id="raceid_clustering" name="Clustering using RaceID" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" > |
2 <description>performs clustering, outlier detection, dimensional reduction</description> | 2 <description>performs clustering, outlier detection, dimensional reduction</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 <import>macros_cheetah.xml</import> | 5 <import>macros_cheetah.xml</import> |
6 </macros> | 6 </macros> |
7 <expand macro="requirements" /> | 7 <expand macro="requirements" /> |
8 <expand macro="version_command_config" prog="cluster.R" cheetah="CLUSTER_CHEETAH" out="&> '$outlog'" /> | 8 <expand macro="version_command_config" prog="cluster.R" cheetah="CLUSTER_CHEETAH" out="&> '$outlog'" /> |
9 | 9 |
10 <inputs> | 10 <inputs> |
11 <param name="inputrds" type="data" format="rdata" label="Input RaceID RDS" help="Requires the RDS output from the normalisation stage" /> | 11 <param name="inputrds" type="data" format="rds" label="Input RaceID RDS" help="Requires the RDS output from the normalisation stage" /> |
12 <section name="clust" title="Clustering" expanded="true" > | 12 <section name="clust" title="Clustering" expanded="true" > |
13 <!-- CompDist --> | 13 <!-- CompDist --> |
14 <param name="metric" type="select" label="Distance Metric" > | 14 <param name="metric" type="select" label="Distance Metric" > |
15 <option value="pearson" selected="true" >Pearson</option> | 15 <option value="pearson" selected="true" >Pearson</option> |
16 <option value="spearman">Spearman</option> | 16 <option value="spearman">Spearman</option> |
77 <param name="pvalue" type="float" min="0" max="1" value="0.01" label="P-value Cutoff" help="P-value cutoff for the inference of differential gene expression" /> | 77 <param name="pvalue" type="float" min="0" max="1" value="0.01" label="P-value Cutoff" help="P-value cutoff for the inference of differential gene expression" /> |
78 </section> | 78 </section> |
79 </inputs> | 79 </inputs> |
80 <outputs> | 80 <outputs> |
81 <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" /> | 81 <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" /> |
82 <data name="outrdat" format="rdata" label="${tool.name} on ${on_string}: RDS" /> | 82 <data name="outrdat" format="rds" label="${tool.name} on ${on_string}: RDS" /> |
83 <data name="outassignments" format="tabular" label="${tool.name} on ${on_string}: Cell-to-Cluster assignments" /> | 83 <data name="outassignments" format="tabular" label="${tool.name} on ${on_string}: Cell-to-Cluster assignments" /> |
84 <data name="outgenelist" format="tabular" label="${tool.name} on ${on_string}: Cluster - Genes per Cluster" /> | 84 <data name="outgenelist" format="tabular" label="${tool.name} on ${on_string}: Cluster - Genes per Cluster" /> |
85 <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Log" > | 85 <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Log" > |
86 <filter>use_log</filter> | 86 <filter>use_log</filter> |
87 </data> | 87 </data> |
93 <assert_contents> | 93 <assert_contents> |
94 <has_line_matching expression=".*ENSDARG00000108379\s+1.*" /> | 94 <has_line_matching expression=".*ENSDARG00000108379\s+1.*" /> |
95 <has_line_matching expression=".*ENSDARG00000027310\s+8.*" /> | 95 <has_line_matching expression=".*ENSDARG00000027310\s+8.*" /> |
96 </assert_contents> | 96 </assert_contents> |
97 </output> | 97 </output> |
98 <output name="outrdat" value="matrix2.rdat" compare="sim_size" delta="500" /> | 98 <output name="outrdat" value="matrix2.rdat" compare="sim_size" delta="40000" /> |
99 <output name="outpdf" value="matrix2.pdf" compare="sim_size" delta="100" /> | 99 <output name="outpdf" value="matrix2.pdf" compare="sim_size" delta="100" /> |
100 <output name="outassignments" > | 100 <output name="outassignments" > |
101 <assert_contents> | 101 <assert_contents> |
102 <has_line_matching expression="P1_B1_ATCCAC\s1\s1\sFALSE" /> | 102 <has_line_matching expression="P1_B1_ATCCAC\s1\s1\sFALSE" /> |
103 </assert_contents> | 103 </assert_contents> |
212 * Good stable clusters should near the 0.8 mark, but 0.6 is acceptable, and for a large number of clusters, one or two low scoring clusters are also acceptable. | 212 * Good stable clusters should near the 0.8 mark, but 0.6 is acceptable, and for a large number of clusters, one or two low scoring clusters are also acceptable. |
213 * Heatmaps: | 213 * Heatmaps: |
214 * The initial and final clustering (as determined using random forest) | 214 * The initial and final clustering (as determined using random forest) |
215 * For each of the most differentially expressed genes in each cluster | 215 * For each of the most differentially expressed genes in each cluster |
216 | 216 |
217 The tool requires the RData input from the previous filtering / normalisation / confounder removal step to work. | 217 The tool requires the RDS input from the previous filtering / normalisation / confounder removal step to work. |
218 | 218 |
219 | 219 |
220 ]]> | 220 ]]> |
221 </help> | 221 </help> |
222 <expand macro="citations" /> | 222 <expand macro="citations" /> |