Mercurial > repos > iuc > multiqc
annotate gatk_plugin.xml @ 24:f7e2f1eb3a16 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
author | iuc |
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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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changeset
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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 <token name="@GATK_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( $repeat.software_cond.output ) |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
diff
changeset
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4 #if str($repeat2.type) == "varianteval" |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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5 #set $pattern = "#:GATKTable:TiTvVariantEvaluator" |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
diff
changeset
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6 @LN_2_FILES@ |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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diff
changeset
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7 #elif str($repeat2.type) == "base_recalibrator" |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
diff
changeset
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8 #set $pattern = "#:GATKTable:Arguments:Recalibration" |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
diff
changeset
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9 @LN_2_FILES@ |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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changeset
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10 #end if |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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changeset
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11 #end for |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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changeset
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12 ]]></token> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
diff
changeset
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13 <xml name="gatk_form"> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
diff
changeset
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14 <repeat name="output" title="GATK output" min="1"> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
diff
changeset
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15 <param name="type" type="select" label="Type of GATK output?"> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
diff
changeset
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16 <option value="varianteval">Variant eval file</option> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
diff
changeset
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17 <option value="base_recalibrator">Base recalibrator file</option> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
diff
changeset
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18 </param> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
diff
changeset
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19 <param name="input" type="data" format="txt" multiple="true" label="GATK output"/> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
diff
changeset
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20 </repeat> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
diff
changeset
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21 </xml> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
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changeset
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22 <!-- 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
parents:
diff
changeset
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23 <xml name="gatk_test"> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
diff
changeset
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24 <test expect_num_outputs="3"> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
diff
changeset
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25 <repeat name="results"> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
diff
changeset
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26 <conditional name="software_cond"> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
diff
changeset
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27 <param name="software" value="gatk"/> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
diff
changeset
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28 <repeat name="output"> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
diff
changeset
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29 <param name="type" value="base_recalibrator"/> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
diff
changeset
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30 <param name="input" value="gatk_BaseRecalibrator.txt"/> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
diff
changeset
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31 </repeat> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
diff
changeset
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32 <repeat name="output"> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
diff
changeset
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33 <param name="type" value="varianteval"/> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
diff
changeset
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34 <param name="input" value="gatk_varianteval.txt"/> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
diff
changeset
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35 </repeat> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
diff
changeset
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36 </conditional> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
diff
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37 </repeat> |
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="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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39 <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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40 <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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41 <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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42 <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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43 <assert_contents> |
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="Title of the report"/> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
diff
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45 <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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46 <has_text text="gatk_varianteval_variant_plot"/> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
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47 </assert_contents> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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48 </output> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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49 <output name="stats"> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
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50 <assert_contents> |
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="gatk_varianteval_txt"/> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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52 <has_n_lines n="2"/> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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53 <has_n_columns n="3"/> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
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54 </assert_contents> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
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55 </output> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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56 <output_collection name="plots" type="list" count="4"/> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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57 </test> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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58 </xml> |
f7e2f1eb3a16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
parents:
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59 </macros> |