Mercurial > repos > iuc > multiqc

annotate bismark_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
parents:
diff changeset
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 <token name="@BISMARK_COMMAND@"><![CDATA[
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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3 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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4 @CREATE_REPEAT_DIR_1@
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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5 #if str($repeat2.type) == "align"
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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6 #for $file in $repeat2.input
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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7 @ESCAPE_IDENTIFIER@
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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8 #set file_path = os.path.join($repeat_dir, str($identifier) + '_SE_report.txt')
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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9 ln -s '$file' '$file_path' &&
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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10 #end for
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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11 #elif str($repeat2.type) == "dedup"
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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12 #for $file in $repeat2.input
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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13 @ESCAPE_IDENTIFIER@
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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14 #set file_path = os.path.join($repeat_dir, str($identifier) + '_deduplication_report.txt')
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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15 ln -s '$file' '$file_path' &&
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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16 #end for
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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17 #elif str($repeat2.type) == "meth_extract"
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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18 #for $file in $repeat2.input
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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19 @ESCAPE_IDENTIFIER@
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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20 #set file_path = os.path.join($repeat_dir, str($identifier) + '_splitting_report.txt')
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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21 ln -s '$file' '$file_path' &&
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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22 #end for
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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23 #elif str($repeat2.type) == "m_bias"
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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24 #for $file in $repeat2.input
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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25 @ESCAPE_IDENTIFIER@
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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26 #set file_path = os.path.join($repeat_dir, str($identifier) + '_M-bias.txt')
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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27 ln -s '$file' '$file_path' &&
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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28 #end for
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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29 #elif str($repeat2.type) == "bam2nuc"
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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30 #for $file in $repeat2.input
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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31 @ESCAPE_IDENTIFIER@
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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32 #set file_path = os.path.join($repeat_dir, str($identifier) + '.nucleotide_stats.txt')
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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33 ln -s '$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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34 #end for
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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35 #end if
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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36 #end for
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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37 ]]></token>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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38 <xml name="bismark_form">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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39 <repeat name="output" title="Bismark output" min="1">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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40 <param name="type" type="select" label="Type of Bismark output?">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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41 <option value="align">Alignment file</option>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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42 <option value="dedup">Deduplication file</option>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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43 <option value="meth_extract">Methylation file</option>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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44 <option value="m_bias">m_bias file</option>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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45 <option value="bam2nuc">bam2nuc file</option>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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46 </param>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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47 <param name="input" type="data" format="txt" multiple="true" label="Bismark output"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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48 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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49 </xml>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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50 <!-- 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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51 <xml name="bismark_test">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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52 <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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53 <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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54 <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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55 <param name="software" value="bismark"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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56 <repeat name="output">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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57 <param name="type" value="align"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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58 <param name="input" value="bismark.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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59 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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60 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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61 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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62 <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
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63 <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
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64 <param name="flat" value="true"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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65 <param name="export" value="true"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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66 <output name="html_report">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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67 <assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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68 <has_text text="Title of the report"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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69 <has_text text="Commment for the report"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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70 <has_text text="bismark-alignment"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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71 </assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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72 </output>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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73 <output name="stats">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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74 <assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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75 <has_text text="bismark_txt_SE_report"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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76 <has_n_lines n="2"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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77 <has_n_columns n="3"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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78 </assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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79 </output>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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80 <output_collection name="plots" type="list" count="0"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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81 </test>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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82 </xml>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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83 </macros>