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annotate macros.xml @ 0:099b0b7ea9da draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
author bgruening
date Thu, 26 Mar 2020 20:07:29 +0000
parents
children 2cf5ca0524ed
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099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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1 <macros>
099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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2 <token name="@CP_VERSION@">3.1.9</token>
099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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3 <token name="@PY_VERSION@">2.7.16</token>
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4 <token name="@FORMATS@">jpg,png,tiff,bmp,gif,pcx,ppm,psd,pbm,pgm,eps</token>
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099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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6 <token name="@SPACES@">" "</token> <!-- four spaces needed for CP pipeline file -->
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099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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8 <xml name="output_pipeline_macro">
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9 <data name="out_file" from_work_dir="output" format="txt" label="Output pipeline" />
099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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10 </xml>
099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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12 <xml name="input_pipeline_macro">
099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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13 <param name="input_pipeline" type="data" format="data" label="Pipeline to select"/>
099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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14 </xml>
099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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16 <xml name="cp_requirements">
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17 <requirements>
099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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18 <requirement type="package" version="@CP_VERSION@">cellprofiler</requirement>
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19 </requirements>
099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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20 </xml>
099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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22 <xml name="py_requirements">
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23 <requirements>
099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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24 <requirement type="package" version="@PY_VERSION@">python</requirement>
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25 </requirements>
099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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26 </xml>
099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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28 <xml name="citations">
099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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29 <citations>
099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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30 <citation type="bibtex">
099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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31 @misc{galaxytoolscellprofiler,
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32 author = {Sun, Yi},
099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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33 year = {2020},
099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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34 title = {Cellprofiler Galaxy tools},
099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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35 publisher = {Github},
099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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36 journal = {Github repository},
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37 url = {https://github.com/bgruening/galaxytools/tools/cellrprofiler},
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38 }
099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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39 </citation>
099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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40 </citations>
099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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41 </xml>
099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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43 <xml name="cmd_modules">
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44 <command detect_errors="aggressive"><![CDATA[
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45 python '$script_file' '$inputs' '$input_pipeline'
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46 ]]></command>
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47 </xml>
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49 <xml name="text_validator">
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50 <validator type="regex" message="Only numbers, letters, hyphen, underscore and spaces are allowed">^[A-Za-z0-9 _-]*$</validator>
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51 </xml>
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53 <xml name="test_input_pipeline_param">
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54 <param name="input_pipeline" value="common.txt" />
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55 </xml>
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57 <xml name="test_out_file" token_file="common.txt">
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58 <output name="out_file" ftype="txt" file="@FILE@" lines_diff="0"/>
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59 </xml>
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099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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61 <xml name="help" token_module="common">
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62 <help>
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63 This tool appends the inputs of the @MODULE@ module to an existing pipeline file (.cppipe)
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64
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65 Input: existing pipeline file
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66
099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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67 Output: new pipeline file
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099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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69 Combine this tool with "Common" tool and "CellProfiler" tool together to run the current module alone.
099b0b7ea9da "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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70 </help>
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71 </xml>
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72 </macros>
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