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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
author azomics
date Thu, 23 Jul 2020 08:58:29 -0400
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62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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1 <tool id="get_profiles_cell_ontology" name="Associate FLOCK populations" version="1.1+galaxy0" profile="18.01">
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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2 <description>with cell ontology</description>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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3 <requirements>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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4 <requirement type="package" version="2.11.2">jinja2</requirement>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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5 <requirement type="package" version="1.26.0">bioconductor-flowcl</requirement>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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6 </requirements>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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7 <stdio>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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8 <exit_code range="2" level="fatal" description="There was a problem running flowCL. You might want to check your marker names - See stderr for more details." />
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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9 <exit_code range="3:" level="fatal" description="See stderr for more details." />
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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10 </stdio>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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11 <command><![CDATA[
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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12 python '$__tool_directory__/profileCLs.py' -i '${input}' -o '${html_file}' -d '${html_file.files_path}' -t '$__tool_directory__'
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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13 ]]>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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14 </command>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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15 <inputs>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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16 <param format="flowscore" name="input" type="data" label="Population score profiles from FLOCK"/>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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17 </inputs>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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18 <outputs>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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19 <data format="html" name="html_file" label="Cell ontology of ${input.name}">
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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20 </data>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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21 </outputs>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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22 <tests>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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23 <test>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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24 <param name="input" value="input.flowscore"/>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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25 <output name="html_file" file="out.html">
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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26 <extra_files type="file" name="CLprofiles.txt" value="CLprofiles.txt"/>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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27 <extra_files type="file" name="flowcl_pop01.pdf" value="flowcl_pop01.pdf" compare="sim_size"/>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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28 <extra_files type="file" name="flowcl_pop01.txt" value="flowcl_pop01.txt"/>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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29 <extra_files type="file" name="flowcl_pop03.pdf" value="flowcl_pop03.pdf" compare="sim_size"/>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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30 <extra_files type="file" name="flowcl_pop03.txt" value="flowcl_pop03.txt"/>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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31 <extra_files type="file" name="scores.txt" value="scores.txt"/>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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32 </output>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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33 </test>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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34 </tests>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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35 <help><![CDATA[
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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36 This tool uses flowCL to find a match for each of the populations defined by FLOCK.
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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37 .. class:: warningmark
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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38 Please note that the scores computed for each markers and population correspond to quartiles binning, and not necessarily to what would be considered +, -, low or high.
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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39 -----
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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40 **Input**
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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41 This tool reads in the population score profiles from FLOCK.
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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42 .. class:: warningmark
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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43 **The marker names need to be in the cell ontology for this to work**
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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44 **Output**
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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45 The output is a page that allows visualization of the data.
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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46 -----
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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47 **Example**
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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48 *Input*
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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49 *Population profile file*::
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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50 Population_ID Marker1 Marker2 Marker3 ... Count Percentage
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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51 1 1 3 2 ... 3885 6.44
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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52 2 1 3 4 ... 2774 4.62
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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53 3 2 2 3 ... 2151 3.59
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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54 4 1 3 2 ... 1207 2.01
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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55 ... ... ... ... ... ... ...
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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56 *Output*
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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57 The CL terms hyperlink to their representation in the Immport Cell Ontology browser. The full flowCL run summary is accessible by clicking on the phenotype.
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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58 .. image:: ../../static/images/flowtools/profileCL.png
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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59 .. image:: ../../static/images/flowtools/popprofiles.png
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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60 ]]>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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61 </help>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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62 <citations>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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63 <citation type="doi">10.1093/bioinformatics/btu807</citation>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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64 </citations>
62d8985a41e2 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/profile_cl commit 5cdc32e68f9ec685f9890902c5ecc75047248361"
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65 </tool>