Mercurial > repos > iuc > raceid_inspecttrajectory

comparison raceid_inspecttrajectories.xml @ 6:c8434a623268 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
author iuc
date Thu, 15 Apr 2021 18:58:58 +0000
parents 86e2358cf273
children 3478133d0f6f
comparison
equal deleted inserted replaced
5:69018f285aa3 6:c8434a623268
1 <tool id="raceid_inspecttrajectory" name="Lineage Branch Analysis using StemID" version="@VERSION_RACEID@.@VERSION_WRAPPER@" > 1 <tool id="raceid_inspecttrajectory" name="Lineage Branch Analysis using StemID" version="@VERSION_RACEID@+galaxy@VERSION_WRAPPER@" >
2 <description>inspects branches of a lineage tree</description> 2 <description>inspects branches of a lineage tree</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>
88 <filter>trjsid['basic']['doit'] == "yes"</filter> 88 <filter>trjsid['basic']['doit'] == "yes"</filter>
89 </data> 89 </data>
90 <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Log" > 90 <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Log" >
91 <filter>use_log</filter> 91 <filter>use_log</filter>
92 </data> 92 </data>
93
94 </outputs> 93 </outputs>
95 <tests> 94 <tests>
96 <test> 95 <test>
97 <!-- default, generates a blank report --> 96 <!-- default, generates a blank report -->
98 <param name="inputrds" value="out_traject_default.ltree.rdat" /> 97 <param name="inputrds" value="out_traject_default.ltree.rdat" />
106 <param name="doit" value="yes" /> 105 <param name="doit" value="yes" />
107 <param name="i" value="3" /> 106 <param name="i" value="3" />
108 <param name="br" value="1,3,8" /> 107 <param name="br" value="1,3,8" />
109 </conditional> 108 </conditional>
110 </section> 109 </section>
111 <output name="outpdf" value="out_traject_inspect_stemid.pdf" compare="sim_size" delta="30" /> 110 <output name="outpdf" value="out_traject_inspect_stemid.pdf" compare="sim_size" delta="500" />
112 <output name="outdiffgenes" value="out_traject_inspect_stemid.tabular" /> 111 <output name="outdiffgenes" value="out_traject_inspect_stemid.tabular" />
113 </test> 112 </test>
114 <test> 113 <test>
115 <!-- fateID trajectory inspection: vignette search "cellsfromtree" --> 114 <!-- fateID trajectory inspection: vignette search "cellsfromtree" -->
116 <param name="inputrds" value="out_traject_default.ltree.rdat" /> 115 <param name="inputrds" value="out_traject_default.ltree.rdat" />
124 <param name="getsom_alpha" value="0.5" /> 123 <param name="getsom_alpha" value="0.5" />
125 <param name="plotheat_xlab" value="true" /> 124 <param name="plotheat_xlab" value="true" />
126 </expand> 125 </expand>
127 </conditional> 126 </conditional>
128 </section> 127 </section>
129 <output name="outpdf" value="out_traject_inspect_fateid.pdf" compare="sim_size" delta="15" /> 128 <output name="outpdf" value="out_traject_inspect_fateid.pdf" compare="sim_size" delta="500" />
130 </test> 129 </test>
131 <test> 130 <test>
132 <!-- fateID trajectory inspection with som: vignette search "SOM" --> 131 <!-- fateID trajectory inspection with som: vignette search "SOM" -->
133 <param name="inputrds" value="out_traject_default.ltree.rdat" /> 132 <param name="inputrds" value="out_traject_default.ltree.rdat" />
134 <section name="trjfid" > 133 <section name="trjfid" >
142 <param name="use_genes" value="12" /> 141 <param name="use_genes" value="12" />
143 </expand> 142 </expand>
144 </conditional> 143 </conditional>
145 </conditional> 144 </conditional>
146 </section> 145 </section>
147 <output name="outpdf" value="out_traject_inspect_fateid_som.pdf" compare="sim_size" delta="15" /> 146 <output name="outpdf" value="out_traject_inspect_fateid_som.pdf" compare="sim_size" delta="500" />
148 </test> 147 </test>
149 <test> 148 <test>
150 <!-- uses all 3 sections with additional non-default params --> 149 <!-- uses all 3 sections with additional non-default params -->
151 <param name="inputrds" value="out_traject_default.ltree.rdat" /> 150 <param name="inputrds" value="out_traject_default.ltree.rdat" />
152 <section name="trjsid" > 151 <section name="trjsid" >
183 </conditional> 182 </conditional>
184 </conditional> 183 </conditional>
185 </conditional> 184 </conditional>
186 </section> 185 </section>
187 <output name="outdiffgenes" value="out_traject_inspect_allthree.tabular" /> 186 <output name="outdiffgenes" value="out_traject_inspect_allthree.tabular" />
188 <output name="outpdf" value="out_traject_inspect_allthree.pdf" compare="sim_size" delta="15" /> 187 <output name="outpdf" value="out_traject_inspect_allthree.pdf" compare="sim_size" delta="500" />
189 </test> 188 </test>
190 </tests> 189 </tests>
191 <help><![CDATA[ 190 <help><![CDATA[
192 StemID2 and FateID 191 StemID2 and FateID
193 ===================== 192 =====================