Mercurial > repos > ebi-gxa > ct_check_labels

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
author ebi-gxa
date Fri, 27 Nov 2020 13:37:20 +0000
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733ef9ca2455 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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1 <tool id="ct_check_labels" name="Cell types - check labels" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
733ef9ca2455 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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2 <description>filters non-alphanumeric characters from labels</description>
733ef9ca2455 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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3 <macros>
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4 <import>ct_macros.xml</import>
733ef9ca2455 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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5 </macros>
733ef9ca2455 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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9 check_labels.R --input-file "${input_file}" --condensed "${condensed}" --attribute-type-col-num "${attribute_type_col_num}" --variable-col-num "${variable_col_num}" --avoid-lowercase "${avoid_lowercase}" --output-path "${output_path}"
733ef9ca2455 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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10
733ef9ca2455 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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11 #if $label_field
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12 --label-field "${label_field}"
733ef9ca2455 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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13 #end if
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15 ]]></command>
733ef9ca2455 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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16 <inputs>
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18 <param type="data" name="input_file" label="Input File" multiple="true" format="txt" help="Input metadta file" />
733ef9ca2455 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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19 <param type="text" name="label_field" label="Label Field" optional="true" help="Name of label field in metadata file">
733ef9ca2455 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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20 <expand macro="sanitize_strings" />
733ef9ca2455 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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21 </param>
733ef9ca2455 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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22 <param type="boolean" name="condensed" checked="false" label="Condensed Metadata File" help="Are the supplied metadata files of condensed format?" />
733ef9ca2455 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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23 <param type="integer" name="attribute_type_col_num" value='5' label="Number of Attribute Type Column" help="Number of the attribute type field in condensed metadata file. Default: 5" />
733ef9ca2455 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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24 <param type="integer" name="variable_col_num" value='6' label="Number of Label Column" help="Number of the label field in condensed metadata file. Default: 6" />
733ef9ca2455 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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25 <param type="boolean" name="avoid_lowercase" checked="false" label="Avoid Lowercaase" help="Should setting the labels to lowercase be skipped? Default: False" />
733ef9ca2455 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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26
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27 </inputs>
733ef9ca2455 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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28 <outputs>
733ef9ca2455 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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29 <data name="output_path" format="txt" />
733ef9ca2455 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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30 </outputs>
733ef9ca2455 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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31 <tests>
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32 <test>
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33 <param name="input_file" value="SDRFs/E-ENAD-27.condensed-sdrf.tsv" />
733ef9ca2455 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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34 <param name="label_field" value="inferred cell type" />
733ef9ca2455 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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35 <param name="condensed" value="TRUE" />
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36 <output name="output_path" file="checked_SDRF.tsv" compare="sim_size" />
733ef9ca2455 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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37 </test>
733ef9ca2455 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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38 </tests>
733ef9ca2455 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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39 <help><![CDATA[
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40 @HELP@
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41
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42 @VERSION_HISTORY@
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43 ]]></help>
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44 <expand macro="citations" />
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45 </tool>