Mercurial > repos > iuc > multiqc

annotate salmon_plugin.xml @ 24:f7e2f1eb3a16 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
author iuc
date Mon, 02 Sep 2024 14:22:54 +0000
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24
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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1 <macros>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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2 <!-- not yet finished -->
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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3 <token name="@SALMON_COMMAND@"><![CDATA[
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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4 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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5 @CREATE_REPEAT_DIR_2@
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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6 #if str($repeat2.type.type) == "meta"
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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7 #for $k, $file in enumerate($repeat2.type.input)
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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8 #set file_dir = os.path.join($repeat_dir, 'file_' + str($k))
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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9 #set file_path = os.path.join($file_dir, 'meta_info.json')
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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10 mkdir '$file_dir' &&
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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11 ln -s '$file' '$file_path' &&
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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12 #end for
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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13 #elif str($repeat2.type.type) == "fld"
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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14 #for $k, $file in enumerate($repeat2.type.input)
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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15 #set file_dir = os.path.join($repeat_dir, 'file_' + str($k))
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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16 #set file_path = os.path.join($file_dir,'flenDist.txt')
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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17 mkdir '$file_dir' &&
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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18 ln -s '$file' '$file_path' &&
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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19 #end for
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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20 #end if
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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21 #end for
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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22 ]]></token>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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23 <xml name="salmon_form">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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24
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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25 </xml>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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26 <!-- add here your test files and tests, the more stringent the better -->
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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27 <xml name="salmon_test">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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28 <test expect_num_outputs="3">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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29 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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30 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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31 <param name="software" value="trimmomatic"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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32 <param name="input" value="trimmomatic.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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33 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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34 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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35 <param name="title" value="Title of the report"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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36 <param name="comment" value="Commment for the report"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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37 <param name="flat" value="true"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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38 <param name="export" value="true"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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39 <output name="html_report">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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40 <assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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41 <has_text text="Title of the report"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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42 <has_text text="Commment for the report"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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43 <has_text text="cutadapt_trimmed_sequences_plot"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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44 <has_text text="All-in-one FASTQ preprocessor"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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45 <has_text text="trimmomatic_plot"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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46 </assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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47 </output>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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48 <output name="stats">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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49 <assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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50 <has_text text="dataset_33"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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51 <has_text text="R1_fq"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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52 <has_text text="result_right"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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53 <has_text text="25839_merged"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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54 <has_text text="C2"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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55 <has_n_lines n="11"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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56 <has_n_columns n="22"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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57 </assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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58 </output>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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59 <output_collection name="plots" type="list" count="29"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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60 </test>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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61 </xml>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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62 </macros>