Mercurial > repos > iuc > export2graphlan
annotate export2graphlan.xml @ 0:ed1becc01910 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
author | iuc |
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date | Sat, 04 Mar 2017 11:44:38 -0500 |
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children | b16989c1e3a7 |
rev | line source |
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0
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
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1 <tool id="export2graphlan" name="Export to GraPhlAn" version="0.19"> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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2 <description></description> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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3 <requirements> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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4 <requirement type="package" version="0.19">export2graphlan</requirement> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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changeset
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5 </requirements> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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6 <stdio> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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7 </stdio> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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8 <version_command> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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9 <![CDATA[ |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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10 export2graphlan.py -v |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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changeset
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11 ]]> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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changeset
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12 </version_command> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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changeset
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13 <command> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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14 <![CDATA[ |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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changeset
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15 export2graphlan.py |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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changeset
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16 --lefse_input '$lefse_input' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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17 #if $input_lefse_output.input_lefse_output_test == "true" |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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18 --lefse_output '$input_lefse_output.lefse_output' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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19 #end if |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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changeset
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20 -t '$tree' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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21 -a '$annotation' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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changeset
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22 #if $annotations |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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changeset
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23 --annotations '$annotations' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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24 #end if |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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changeset
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25 #if $external_annotations |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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changeset
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26 --external_annotations '$external_annotations' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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changeset
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27 #end if |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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changeset
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28 #if $background_levels |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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changeset
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29 --background_levels '$background_levels' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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changeset
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30 #end if |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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changeset
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31 #if $background_clades |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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changeset
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32 --background_clades '$background_clades' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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changeset
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33 #end if |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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changeset
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34 #if $background_colors |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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changeset
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35 --background_colors '$background_colors' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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36 #end if |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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37 #if $title |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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38 --title '$title' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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39 #end if |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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40 |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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41 --title_font_size '$title_font_size' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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42 --def_clade_size '$def_clade_size' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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43 --min_clade_size '$min_clade_size' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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44 --max_clade_size '$max_clade_size' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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45 --def_font_size '$def_font_size' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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46 --min_font_size '$min_font_size' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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47 --max_font_size '$max_font_size' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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48 --annotation_legend_font_size '$annotation_legend_font_size' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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49 --abundance_threshold '$abundance_threshold' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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50 |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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51 #if $most_abundant |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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52 --most_abundant '$most_abundant' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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53 #end if |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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54 #if $least_biomarkers |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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55 --least_biomarkers '$least_biomarkers' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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56 #end if |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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57 |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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58 --fname_row '$fname_row' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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59 --sname_row '$sname_row' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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60 |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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61 #if $metadata_rows |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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62 --metadata_rows '$metadata_rows' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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63 #end if |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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64 #if $skip_rows |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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65 --skip_rows '$skip_rows' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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66 #end if |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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67 #if $sperc |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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68 --sperc '$sperc' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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69 #end if |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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70 #if $fperc |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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71 --fperc '$fperc' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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72 #end if |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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73 #if $stop |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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74 --stop '$stop' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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75 #end if |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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76 #if $ftop |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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77 --ftop '$ftop' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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78 #end if |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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79 ]]> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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80 </command> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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81 <inputs> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
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82 <param argument="--lefse_input" type="data" format="tabular,txt,tsv" label="Input file" help="Identical to LEfSe input file"/> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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83 <conditional name="input_lefse_output"> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
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84 <param name="input_lefse_output_test" type="select" label="Use a LEfSe output file as input?" help=""> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
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85 <option value="true">Yes</option> |
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86 <option value="false" selected="true">No</option> |
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87 </param> |
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88 <when value="true"> |
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89 <param argument="--lefse_output" type="data" format="tabular" label="Input file corresponding to LEfSe output file"/> |
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90 </when> |
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91 <when value="false"/> |
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92 </conditional> |
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93 <param argument="--annotations" type="text" label="List which levels should be annotated in the tree" help="The levels must be in comma-separated form" optional="True"/> |
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94 <param argument="--external_annotations" type="text" label="List which levels should use the external legend for the annotation" help="The levels must be in comma-separated form" optional="True"/> |
ed1becc01910
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95 <param argument="--background_levels" type="text" label="List which levels should be highlight with a shaded background" help="The levels must be in comma-separated form" optional="True"/> |
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96 <param argument="--background_clades" type="text" label="List of the clades that should be highlight with a shaded background" help="The clades must be in comma-separated form" optional="True"/> |
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97 <param argument="--background_colors" type="text" label="List of color to use for the shaded background" help="Colors can be either in RGB or HSV (using a semi-colon to separate values, surrounded with ()). The different colors must be in comma-separated form" optional="True"/> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
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98 <param argument="--title" type="text" label="Title of the GraPhlAn plot" optional="True"/> |
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99 <param argument="--title_font_size" type="integer" value="15" label="Title font size"/> |
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100 <param argument="--def_clade_size" type="integer" value="10" label="Default size for clades that are not found as biomarkers"/> |
ed1becc01910
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101 <param argument="--min_clade_size" type="integer" value="20" label="Minimum value of clades that are biomarkers"/> |
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102 <param argument="--max_clade_size" type="integer" value="200" label="Maximum value of clades that are biomarkers"/> |
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103 <param argument="--def_font_size" type="integer" value="10" label="Default font size"/> |
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104 <param argument="--min_font_size" type="integer" value="8" label="Minimum font size"/> |
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105 <param argument="--max_font_size" type="integer" value="12" label="Maximum font size"/> |
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106 <param argument="--annotation_legend_font_size" type="integer" value="10" label="Font size for the annotation legend"/> |
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107 <param argument="--abundance_threshold" type="float" value="20.0" label="Minimun abundance value for a clade to be annotated"/> |
ed1becc01910
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108 <param argument="--most_abundant" type="integer" label="Number of clades to highlight" optional="True"/> |
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109 <param argument="--least_biomarkers" type="integer" label="Minimum number of biomarkers to extract" help=" The taxonomy is parsed, and the level is choosen in order to have at least the specified number of biomarkers" optional="True"/> |
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110 <param argument="--fname_row" type="integer" value="0" label="Row number containing the names of the features" help="-1 specifies that no names are present in the matrix"/> |
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111 <param argument="--sname_row" type="integer" value="0" label="Row number containing the names of the samples" help="-1 specifies that no names are present in the matrix"/> |
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112 <param argument="--metadata_rows" type="integer" label="Row number to use as metadata" optional="True"/> |
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113 <param argument="--skip_rows" type="text" label="Row number to skip from the input file" help="The row numbers are indexed to 0 and comma separated" optional="True"/> |
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114 <param argument="--sperc" type="float" label="Percentile of sample value distribution for sample selection" optional="True"/> |
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115 <param argument="--fperc" type="float" label="Percentile of feature value distribution for sample selection" optional="True"/> |
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116 <param argument="--stop" type="integer" label="Number of top samples to select" help="The order is based on percentile specified by --sperc" optional="True"/> |
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117 <param argument="--ftop" type="integer" label="Number of top features to select" help="The order is based on percentile specified by --fperc" optional="True"/> |
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118 </inputs> |
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119 <outputs> |
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120 <data format="txt" name="tree" label="${tool.name} on ${on_string}: Tree" /> |
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121 <data format="txt" name="annotation" label="${tool.name} on ${on_string}: Annotation" /> |
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122 </outputs> |
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123 <tests> |
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124 <test> |
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125 <param name="lefse_input" value="input_profile.tabular"/> |
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126 <param name="input_lefse_output_test" value="no" /> |
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127 <param name="annotations" value=""/> |
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128 <param name="external_annotations" value=""/> |
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129 <param name="background_levels" value=""/> |
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130 <param name="background_clades" value=""/> |
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131 <param name="background_colors" value=""/> |
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132 <param name="title" value=""/> |
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133 <param name="title_font_size" value="15"/> |
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134 <param name="def_clade_size" value="10"/> |
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135 <param name="min_clade_size" value="20"/> |
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136 <param name="max_clade_size" value="200"/> |
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137 <param name="def_font_size" value="10"/> |
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138 <param name="min_font_size" value="8"/> |
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139 <param name="max_font_size" value="12"/> |
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140 <param name="annotation_legend_font_size" value="10"/> |
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141 <param name="abundance_threshold" value="20.0"/> |
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142 <param name="most_abundant" value=""/> |
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143 <param name="least_biomarkers" value=""/> |
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144 <param name="fname_row" value="0"/> |
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145 <param name="sname_row" value="0" /> |
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146 <param name="metadata_rows" value=""/> |
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147 <param name="skip_rows" value=""/> |
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148 <param name="sperc" value=""/> |
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149 <param name="fperc" value=""/> |
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150 <param name="stop" value=""/> |
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151 <param name="ftop" value=""/> |
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152 <output name="annotation" file="annotation_output.txt"/> |
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153 <output name="tree" file="tree_output.txt"/> |
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154 </test> |
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155 </tests> |
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156 <help><![CDATA[ |
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157 |
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158 **What it does** |
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159 |
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160 export2graphlan is a conversion software tool to produce both annotation and tree file for GraPhlAn. It can convert MetaPhlAn, LEfSe, and/or HUMAnN output to GraPhlAn input format |
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161 |
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162 In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. |
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163 |
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164 For more information, check the `user manual <https://bitbucket.org/CibioCM/export2graphlan/overview/>`_. |
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165 |
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166 ]]></help> |
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167 <citations> |
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168 </citations> |
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169 </tool> |