Mercurial > repos > matthias > daa2rma
annotate macros.xml @ 2:102d29c7c5a7 draft default tip
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit 20ad8976adec9d011d21484859258bf1ad22f42e-dirty
| author | matthias |
|---|---|
| date | Wed, 19 Dec 2018 04:44:10 -0500 |
| parents | 2ac9f9b9dd63 |
| children |
| rev | line source |
|---|---|
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
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changeset
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1 <macros> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
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2 <token name="@TOOL_VERSION@">6.12.3</token> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff
changeset
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3 <xml name="requirements"> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff
changeset
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4 <requirements> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff
changeset
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5 <requirement type="package" version="@TOOL_VERSION@">megan</requirement> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
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6 <yield/> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff
changeset
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7 </requirements> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff
changeset
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8 </xml> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff
changeset
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9 <xml name="stdio"> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff
changeset
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10 <stdio> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff
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11 <exit_code level="fatal" range="1:" description="Error"/> |
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2
102d29c7c5a7
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit 20ad8976adec9d011d21484859258bf1ad22f42e-dirty
matthias
parents:
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diff
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12 <regex match="There is insufficient memory for the Java Runtime Environment" source="stdout" level="fatal_oom" description="Out of memory" /> |
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102d29c7c5a7
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit 20ad8976adec9d011d21484859258bf1ad22f42e-dirty
matthias
parents:
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diff
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13 </stdio> |
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0
2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff
changeset
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14 </xml> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff
changeset
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15 <xml name="version_command"> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
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16 <version_command><![CDATA[./daa2rma |& grep version | sed 's/.*version \([0-9.]\+\),.*/\1/']]></version_command> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff
changeset
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17 </xml> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff
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18 <token name="@CLASSIFICATION_UTILS@"><![CDATA[ |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff
changeset
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19 #def get_mapping($var, $category, $target) |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff
changeset
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20 #if $var.has_key($category+$target): |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff
changeset
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21 #set m="" |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff
changeset
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22 #if $var.has_key($category+$target+"_select") and $var[$category+$target+"_select"]=='indexed': |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff
changeset
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23 #if $var[$category+$target] |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff
changeset
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24 #set m=str($var[$category+$target].fields.path) |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff
changeset
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25 #end if |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff
changeset
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26 #else |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff
changeset
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27 #set m=str($var[$category+$target]) |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff
changeset
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28 #end if |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
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29 #if $m!="" and $m!=None and m!="None": |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
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30 #return "--"+$category+$target+" "+$m |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
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31 #end if |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
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32 #else |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
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33 #return "" |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
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34 #end if |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
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35 #end def |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
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36 |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff
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37 #def get_mapping_history_indexed($var, $category, $target): |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff
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38 #if $var.has_key( $category+$target+'_cond' ): |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
diff
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39 #return $get_mapping($var[$category+$target+'_cond'], $category, $target) |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
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40 #else |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
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41 #return $get_mapping($var, $category, $target) |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
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42 #end if |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
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43 #end def |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
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44 |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
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45 #def get_mapping_acc_gi( $section, $category, $target ): |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
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46 #if category in ['gi2','acc2'] and $section.has_key('acc_or_gi_cond'): |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
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47 #return $get_mapping_history_indexed($section.acc_or_gi_cond, $category, $target) |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
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48 #else: |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
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49 #return $get_mapping_history_indexed($section, $category, $target) |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
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50 #end if |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
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51 #end def |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
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52 ]]></token> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
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53 <xml name="mapping" token_varname="myvar" token_label="mylabel"> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
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54 <conditional name="@VARNAME@_cond"> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
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55 <param name="@VARNAME@_select" type="select" label="@LABEL@"> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
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56 <option value="indexed">Use a built-in mapping</option> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
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57 <option value="history">Use a mapping from the history</option> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
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58 </param> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
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59 <when value="indexed"> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
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60 <param argument="--@VARNAME@" type="select" optional="true" label="mapping" > |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
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61 <options from_data_table="megan_tools"> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
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62 <filter type="static_value" column="2" value="@VARNAME@" keep="true"/> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
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63 </options> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
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64 </param> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
parents:
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65 </when> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
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66 <when value="history"> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
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67 <param argument="--@VARNAME@" type="data" format="tabular" optional="true" label="mapping" /> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
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68 </when> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
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69 </conditional> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
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70 </xml> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
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71 <xml name="mappings_gi_acc_syn" token_target="mytarget" token_targetlabel="mytargetlabel"> |
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2ac9f9b9dd63
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty
matthias
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72 <section name="section_@TARGET@" title="@TARGETLABEL@ Mappings" expanded="false"> |
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2ac9f9b9dd63
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73 <conditional name="acc_or_gi_cond"> |
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74 <param name="acc_or_gi_select" type="select" label="Mapping from GI/Accession" help="use GI for NR releases until August 2016, containing GI numbers"> |
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75 <option value="acc">Accession</option> |
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76 <option value="gi">GI</option> |
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77 </param> |
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78 <when value="gi"> |
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79 <expand macro="mapping" varname="gi2@TARGET@" label="GI-to-@TARGETLABEL@ mapping"/> |
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80 </when> |
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81 <when value="acc"> |
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82 <expand macro="mapping" varname="acc2@TARGET@" label="Accession-to-@TARGETLABEL@ mapping"/> |
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83 </when> |
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84 </conditional> |
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85 <expand macro="mapping" varname="syn2@TARGET@" label="Synonyms-to-@TARGETLABEL@ mapping"/> |
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86 <yield/> |
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87 </section> |
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88 </xml> |
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89 |
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90 <xml name="mappings_gi_acc_syn_tags" token_target="mytarget" token_targetlabel="mytargetlabel"> |
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91 <expand macro="mappings_gi_acc_syn" target="@TARGET@" targetlabel="@TARGETLABEL@"> |
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92 <param argument="--tags4@TARGET@" type="data" format="tabular" optional="true" label="Tags for @TARGETLABEL@ id parsing" help="(must set to activate id parsing)"/> |
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93 </expand> |
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94 </xml> |
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95 |
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96 <token name="@MDF_CLI@"><![CDATA[ |
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97 #if $metaDataFile: |
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98 -mdf |
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99 #for $m in $metaDataFile |
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100 #if $m |
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101 '$m' |
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102 #end if |
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103 #end for |
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104 #end if |
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105 ]]></token> |
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106 <xml name="mdf_macro"> |
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107 <param argument="--metaDataFile" type="data" format="tabular" multiple="true" optional="true" label="Files containing metadata to be included in RMA6 files"/> |
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108 </xml> |
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109 |
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110 <token name="@READS_CLI@"><![CDATA[ |
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111 ## Reads |
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112 --paired $reads.paired |
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113 --pairedSuffixLength $reads.pairedSuffixLength |
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114 ]]></token> |
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115 <xml name="reads_macro"> |
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116 <section name="reads" title="Reads Options" expanded="true"> |
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117 <param argument="--paired" type="boolean" truevalue="true" falsevalue="false" checked="false" label="" /> |
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118 <param argument="--pairedSuffixLength" type="integer" value="0" label="Length of name suffix used to distinguish names" help="i.e. first word in header) of read and its mate (use 0 if read and mate have same name" /> |
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119 <yield/> |
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120 </section> |
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121 </xml> |
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122 |
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123 <token name="@PARAMETERS_CLI@"><![CDATA[ |
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124 ##Parameters |
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125 --longReads $params.longReads |
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126 --classify $params.classify |
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127 --minScore $params.minScore |
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128 --maxExpected $params.maxExpected |
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129 --minPercentIdentity $params.minPercentIdentity |
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130 --topPercent $params.topPercent |
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131 --minSupportPercent $params.minSupportPercent |
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132 --minSupport $params.minSupport |
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133 --minPercentReadCover $params.minPercentReadCover |
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134 --minPercentReferenceCover $params.minPercentReferenceCover |
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135 --lcaAlgorithm $params.lcaAlgorithm |
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136 --lcaCoveragePercent $params.lcaCoveragePercent |
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137 --readAssignmentMode $params.readAssignmentMode |
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138 #if $params.conFile: |
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139 --conFile '$params.conFile' |
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140 #end if |
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141 ]]></token> |
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142 <xml name="params_macro"> |
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143 <section name="params" title="Parameters" expanded="true"> |
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144 <param argument="--longReads" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Parse and analyse as long reads" /> |
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145 <yield/> |
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146 <param argument="--classify" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Run classification algorithm" /> |
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147 <param argument="--minScore" type="float" value="50.0" label="Min score" /> |
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148 <param argument="--maxExpected" type="float" value="0.01" label="Max expected" /> |
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149 <param argument="--minPercentIdentity" type="float" value="0.00" label="Min percent identity" /> |
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150 <param argument="--topPercent" type="float" value="10.0" label="Top percent" /> |
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151 <param argument="--minSupportPercent" type="float" value="0.05" label="Min support as percent of assigned reads (0==off)" /> |
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152 <param argument="--minSupport" type="integer" value="0" label="Min support (0==off)" /> |
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153 <param argument="--minPercentReadCover" type="float" value="0.0" label="Min percent of read length to be covered by alignments" /> |
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154 <param argument="--minPercentReferenceCover" type="float" value="0.0" label="Min percent of reference length to be covered by alignments" /> |
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155 <param argument="--lcaAlgorithm" type="select" label="LCA algorithm to use for taxonomic assignment"> |
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156 <option value="naive" selected="true">naive</option> |
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157 <option value="weighted">weighted</option> |
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158 <option value="longReads">longReads</option> |
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159 </param> |
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160 <param argument="--lcaCoveragePercent" type="float" value="100.0" min="0.0" max="100.0" label="Set the percent for the LCA to cover" /> |
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161 <param argument="--readAssignmentMode" type="select" label="Read assignment mode"> |
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162 <option value="readCount" selected="true">readCount</option> |
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163 <option value="readLength">readLength</option> |
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164 <option value="alignedBases">alignedBases</option> |
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165 <option value="readMagnitude">readMagnitude</option> |
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166 </param> |
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167 <param argument="--conFile" type="data" format="tabular" optional="true" label="File of contaminant taxa" help="one Id or name per line"/> |
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168 </section> |
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169 </xml> |
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170 |
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171 <token name="@CLASSIFICATION_CLI@"><![CDATA[ |
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172 ##Classification support: |
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173 --parseTaxonNames $classification.parseTaxonNames |
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174 #for $cat in $CATEGORIES: |
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175 #for $target in $TARGETS |
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176 $get_mapping_acc_gi( $classification['section_'+$target], $cat, $target ) |
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177 #end for |
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178 #end for |
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179 ]]></token> |
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180 <xml name="classification_macro"> |
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181 <section name="classification" title="Classification support options" expanded="true"> |
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182 <param argument="--parseTaxonNames" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Parse taxon names" /> |
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183 |
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184 <expand macro="mappings_gi_acc_syn" target="taxa" targetlabel="Taxonomy"/> |
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185 <expand macro="mappings_gi_acc_syn_tags" target="eggnog" targetlabel="EGGNOG"/> |
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186 <expand macro="mappings_gi_acc_syn_tags" target="interpro2go" targetlabel="INTERPRO2GO"/> |
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187 <expand macro="mappings_gi_acc_syn_tags" target="seed" targetlabel="SEED"/> |
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188 <expand macro="mappings_gi_acc_syn_tags" target="kegg" targetlabel="KEGG"/> |
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189 </section> |
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190 </xml> |
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191 |
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192 <token name="@OTHER_CLI@"><![CDATA[ |
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193 ##Other: |
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194 --firstWordIsAccession $other.firstWordIsAccession |
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195 #if len($other.accessionTags)>0: |
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196 --accessionTags |
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197 #for $i, $s in enumerate($other.accessionTags) |
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198 '$s.tag' |
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199 #end for |
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200 #end if |
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201 ]]></token> |
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202 <xml name="other_macro"> |
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203 <section name="other" title="Other options" expanded="true"> |
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204 <param argument="--firstWordIsAccession" type="boolean" truevalue="true" falsevalue="false" checked="true" label="First word in reference header is accession number" help="enable for NCBI-nr downloaded Sep 2016 or later" /> |
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205 <repeat name="accessionTags" title="List of accession tags" min="0" default="0" help="Default value(s): gb| ref|."> |
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206 <param name="tag" type="text" label="Accession tag"/> |
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207 </repeat> |
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208 </section> |
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209 </xml> |
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210 <xml name="citations"> |
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211 <citations> |
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212 <citation type="doi">10.1038/nmeth.3176</citation> |
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213 <citation type="doi">10.1101/gr.120618.111</citation> |
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214 <citation type="doi">10.1101/gr.5969107</citation> |
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215 <citation type="bibtex"> |
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216 @misc{website, |
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217 author = {Huson et al}, |
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218 year = {TODO}, |
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219 title = {Megan Website}, |
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220 url = {http://ab.inf.uni-tuebingen.de/software/megan6/}, |
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221 }</citation> |
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222 </citations> |
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223 </xml> |
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224 </macros> |