Mercurial > repos > yhoogstrate > crossmap
annotate crossmap.xml @ 7:1efce8a693ca draft default tip
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
| author | yhoogstrate |
|---|---|
| date | Thu, 12 Nov 2015 16:08:56 -0500 |
| parents | 5ef4ac8f2956 |
| children |
| rev | line source |
|---|---|
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5
9da7052375b9
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1
yhoogstrate
parents:
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1 <tool id="crossmap" name="CrossMap" version="0.2.d"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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2 <description>Convert genome coordinates or annotation files between genome assemblies</description> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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3 |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
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4 <requirements> |
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0e0294f5ab3a
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 6e66f1e17650f888c84ec82d100195db61dffdc7-dirty
yhoogstrate
parents:
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5 <requirement type="package" version="312">ucsc_tools</requirement> |
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9c7cc3690f33
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit bdf6760eb0e9d5d9e45908a942383a2ff05bfd09
yhoogstrate
parents:
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6 <requirement type="package" version="2.7">python</requirement> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
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7 <requirement type="package" version="0.2">crossmap</requirement> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
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8 </requirements> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
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9 |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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10 <stdio> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
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11 <regex match="Usage: CrossMap.py" source="stdout" level="fatal"/> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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12 <regex match=".*" source="both" level="log"/> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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13 </stdio> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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14 |
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6
5ef4ac8f2956
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 7ab6217b10b7483a03140eddc9c0567551b41b62
yhoogstrate
parents:
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15 <version_command>python $CROSSMAP_ROOT_DIR/bin/CrossMap.py 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
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16 |
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7
1efce8a693ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
yhoogstrate
parents:
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17 <!-- First line of CrossMap has hardcoded "#!/usr/bin/python". This makes use of Galaxy's python: --> |
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1efce8a693ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
yhoogstrate
parents:
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18 <command><![CDATA[ |
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5
9da7052375b9
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1
yhoogstrate
parents:
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19 python \$CROSSMAP_ROOT_DIR/bin/CrossMap.py |
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0
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
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20 ${multiple.input_format.replace("sam","bam")} |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
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21 |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
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22 #if $multiple.input_format == "vcf" and $multiple.seq_source.index_source == "cached" |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
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23 <!-- This is the 2nd dbkey, and the corresponding value has to be looked up --> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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24 "${filter(lambda x: str( x[1] ) == str($multiple.seq_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }" |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
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25 #else |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
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26 "$multiple.seq_source.input_chain" |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
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27 #end if |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
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28 |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
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29 #if $multiple.input_format in ["bam", "sam"] |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
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30 -m $multiple.insert_size |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
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31 -s $multiple.insert_size_stdev |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
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32 -t $multiple.insert_size_fold |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
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33 #end if |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
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34 |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
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35 "$multiple.seq_source.input" |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
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36 |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
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37 #if $multiple.input_format == "vcf" |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
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38 "$multiple.seq_source.input_fasta" |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
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39 #end if |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
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40 |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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changeset
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41 #if str($multiple.include_fails) == "True" |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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42 > |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
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43 #end if |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
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44 |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
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45 "$output" |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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46 |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
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47 #if $multiple.input_format in ["bam", "sam"] |
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7
1efce8a693ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
yhoogstrate
parents:
6
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48 && mv "${output}.${multiple.input_format}" "$output" |
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1efce8a693ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
yhoogstrate
parents:
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49 && mv "${output}.unmap.${multiple.input_format}" "$output_unmapped" |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
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50 #else if $multiple.input_format in ["vcf"] |
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7
1efce8a693ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
yhoogstrate
parents:
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51 && mv "${output}" "$output" |
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1efce8a693ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
yhoogstrate
parents:
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52 && mv "${output}.unmap" "$output_unmapped" |
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0
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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53 #else if $multiple.input_format in ["wig", "bigwig"] |
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7
1efce8a693ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
yhoogstrate
parents:
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54 && mv "${output}.bw" "$output" |
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1efce8a693ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
yhoogstrate
parents:
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55 && mv "${output}.sorted.bgr" "$output2" |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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56 #end if |
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7
1efce8a693ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
yhoogstrate
parents:
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57 ]]></command> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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58 |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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59 <inputs> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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60 <conditional name="multiple"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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61 <param name="input_format" type="select" label="Convert a file of the following format"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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62 <option value="bam">BAM</option> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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63 <option value="sam">SAM</option> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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64 <option value="bed">BED or BED-like</option> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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65 <option value="bigwig">BigWig</option> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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66 <option value="gff">GFF or GTF</option> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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67 <option value="vcf">VCF</option> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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68 <option value="wig">Wiggle or bedGraph</option> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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69 </param> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
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70 <when value="bam"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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71 <conditional name="seq_source"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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72 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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73 <option value="cached">Local data (in galaxy)</option> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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74 <option value="history">From History</option> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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75 </param> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
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76 <when value="cached"> |
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7
1efce8a693ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
yhoogstrate
parents:
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77 <param type="data" format="bam" name="input" label="BAM file"> |
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0
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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78 <validator type="unspecified_build" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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79 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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parents:
diff
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|
80 </param> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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diff
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81 <param name="input_chain" type="select" label="Lift Over To"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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diff
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82 <options from_file="liftOver.loc"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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83 <column name="name" index="1"/> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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diff
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84 <column name="value" index="2"/> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
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|
85 <column name="dbkey" index="0"/> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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diff
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86 <filter type="data_meta" ref="input" key="dbkey" column="0" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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87 </options> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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88 </param> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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89 </when> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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parents:
diff
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90 <when value="history"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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91 <param type="data" format="bam,sam" name="input" label="BAM/SAM file" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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92 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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93 </when> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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94 </conditional> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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95 |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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96 <param name="insert_size" type="float" value="200.0" label="Insert size (-m)" help="Average insert size of pair-end sequencing (bp) [default=200.0]" /> |
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bfcdabc062ca
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97 <param name="insert_size_stdev" type="float" value="30.0" label="Insert size std. dev (-s)" help="Stanadard deviation of insert size. [default=30.0]" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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98 <param name="insert_size_fold" type="float" value="3.0" label="Insert size std. dev foldchange (-t)" help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean. [default=3.0]" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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99 |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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100 <param name="include_fails" type="hidden" tvalue="False" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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101 </when> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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102 <when value="sam"><!-- BAM and SAM are exactly the same conditions, but they need to be separate to get the proper output format --> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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103 <conditional name="seq_source"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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104 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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105 <option value="cached">Local data (in galaxy)</option> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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106 <option value="history">From History</option> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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107 </param> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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108 <when value="cached"> |
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7
1efce8a693ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
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109 <param type="data" format="sam" name="input" label="SAM file"> |
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0
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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110 <validator type="unspecified_build" /> |
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bfcdabc062ca
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111 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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112 </param> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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113 <param name="input_chain" type="select" label="Lift Over To"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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114 <options from_file="liftOver.loc"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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115 <column name="name" index="1"/> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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116 <column name="value" index="2"/> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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117 <column name="dbkey" index="0"/> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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118 <filter type="data_meta" ref="input" key="dbkey" column="0" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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119 </options> |
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bfcdabc062ca
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120 </param> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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121 </when> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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parents:
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122 <when value="history"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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diff
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123 <param type="data" format="bam,sam" name="input" label="BAM/SAM file" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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124 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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125 </when> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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126 </conditional> |
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bfcdabc062ca
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127 |
|
bfcdabc062ca
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128 <param name="insert_size" type="float" value="200.0" label="Insert size (-m)" help="Average insert size of pair-end sequencing (bp) [default=200.0]" /> |
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bfcdabc062ca
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129 <param name="insert_size_stdev" type="float" value="30.0" label="Insert size std. dev (-s)" help="Stanadard deviation of insert size. [default=30.0]" /> |
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bfcdabc062ca
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130 <param name="insert_size_fold" type="float" value="3.0" label="Insert size std. dev foldchange (-t)" help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean. [default=3.0]" /> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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131 |
|
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132 <param name="include_fails" type="hidden" tvalue="False" /> |
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bfcdabc062ca
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133 </when> |
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bfcdabc062ca
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134 <when value="bed"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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135 <conditional name="seq_source"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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parents:
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136 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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137 <option value="cached">Local data (in galaxy)</option> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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138 <option value="history">From History</option> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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139 </param> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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140 <when value="cached"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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141 <param format="bed" name="input" type="data" label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns."> |
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bfcdabc062ca
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142 <validator type="unspecified_build" /> |
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bfcdabc062ca
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143 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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144 </param> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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145 <param name="input_chain" type="select" label="Lift Over To"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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146 <options from_file="liftOver.loc"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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147 <column name="name" index="1"/> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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148 <column name="value" index="2"/> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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149 <column name="dbkey" index="0"/> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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150 <filter type="data_meta" ref="input" key="dbkey" column="0" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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151 </options> |
|
bfcdabc062ca
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152 </param> |
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bfcdabc062ca
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153 </when> |
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154 <when value="history"> |
|
bfcdabc062ca
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parents:
diff
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155 <param type="data" format="bed" name="input" label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns." /> |
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156 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" /> |
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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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157 </when> |
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158 </conditional> |
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159 |
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160 <param name="include_fails" type="boolean" truevalue="True" checked="false" falsevalue="False" label="Include failed liftovers" help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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161 </when> |
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bfcdabc062ca
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162 <when value="bigwig"> |
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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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163 <conditional name="seq_source"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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164 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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165 <option value="cached">Local data (in galaxy)</option> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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166 <option value="history">From History</option> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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167 </param> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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168 <when value="cached"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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169 <param format="bigwig" name="input" type="data" label="BigWig file"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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170 <validator type="unspecified_build" /> |
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bfcdabc062ca
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171 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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172 </param> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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173 <param name="input_chain" type="select" label="Lift Over To"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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174 <options from_file="liftOver.loc"> |
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bfcdabc062ca
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175 <column name="name" index="1"/> |
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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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176 <column name="value" index="2"/> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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177 <column name="dbkey" index="0"/> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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178 <filter type="data_meta" ref="input" key="dbkey" column="0" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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179 </options> |
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180 </param> |
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bfcdabc062ca
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181 </when> |
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bfcdabc062ca
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182 <when value="history"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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183 <param type="data" format="bigwig" name="input" label="BigWig file" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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184 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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185 </when> |
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186 </conditional> |
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187 |
|
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188 <param name="include_fails" type="hidden" tvalue="False" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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189 </when> |
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bfcdabc062ca
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190 <when value="gff"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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191 <conditional name="seq_source"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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192 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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193 <option value="cached">Local data (in galaxy)</option> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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194 <option value="history">From History</option> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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195 </param> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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196 <when value="cached"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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197 <param format="gtf,gff,gff3" name="input" type="data" label="GTF/GFF file"> |
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bfcdabc062ca
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198 <validator type="unspecified_build" /> |
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199 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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200 </param> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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201 <param name="input_chain" type="select" label="Lift Over To"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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202 <options from_file="liftOver.loc"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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203 <column name="name" index="1"/> |
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bfcdabc062ca
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204 <column name="value" index="2"/> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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205 <column name="dbkey" index="0"/> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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206 <filter type="data_meta" ref="input" key="dbkey" column="0" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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207 </options> |
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208 </param> |
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bfcdabc062ca
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209 </when> |
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bfcdabc062ca
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210 <when value="history"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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211 <param type="data" format="gtf,gff,gff3" name="input" label="GTF/GFF file" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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212 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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213 </when> |
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214 </conditional> |
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215 |
|
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216 <param name="include_fails" type="boolean" truevalue="True" checked="false" falsevalue="False" label="Include failed liftovers" help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')" /> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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217 </when> |
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218 <when value="vcf"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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219 <conditional name="seq_source"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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220 <param name="index_source" type="select" label="Source for LiftOver Data"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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221 <option value="cached">Local data (in galaxy)</option> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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222 <option value="history_chain">Chain file from History</option> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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223 <option value="history_all">Chain & FASTA files from History</option> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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224 </param> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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225 |
|
bfcdabc062ca
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226 <when value="cached"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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227 <param type="data" format="vcf" name="input" label="VCF file"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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228 <validator type="unspecified_build" /> |
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bfcdabc062ca
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229 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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230 </param> |
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bfcdabc062ca
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231 |
|
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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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232 <!-- automatically fetch a FASTA file from the same DBKEY as the chain file --> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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233 <param name="input_chain" type="select" label="Lift Over To (Chain file)"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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diff
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234 <options from_file="liftOver.loc"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
235 <column name="name" index="1" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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diff
changeset
|
236 <column name="value" index="1" /><!-- It is not possible to send the *.chain file as value, and obtain the 2nd dbkey as parameter via a filter --> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
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diff
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237 <column name="dbkey" index="0" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
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diff
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238 <filter type="data_meta" ref="input" key="dbkey" column="0" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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239 </options> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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parents:
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240 </param> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
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241 |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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242 <param name="input_fasta" type="select" label="Lift Over To (FASTA file)" help="The FASTA file must be on the same build (dbkey) as the LiftOver chain file"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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diff
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243 <options from_file="all_fasta.loc"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
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244 <column name="name" index="2"/> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
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245 <column name="value" index="3"/> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
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246 <column name="dbkey" index="1"/> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
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247 <filter type="param_value" ref="input_chain" column="1" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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248 </options> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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parents:
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249 </param> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
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|
250 </when> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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parents:
diff
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251 |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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252 <when value="history_chain"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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253 <param type="data" format="vcf" name="input" label="VCF file"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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254 <validator type="unspecified_build" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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diff
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255 <validator type="dataset_metadata_in_file" filename="all_fasta.loc" metadata_name="dbkey" metadata_column="1" message="LiftOver mapping (FASTA file) is not available for the specified build." /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
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|
256 </param> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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257 <param type="data" format="csv" name="input_chain" multiple="false" label="LiftOver chain file" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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258 <param name="input_fasta" type="select" label="Lift Over To (FASTA file)" help="The FASTA file must be on the same build (dbkey) as the LiftOver chain file"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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diff
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259 <options from_file="all_fasta.loc"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
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diff
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260 <column name="name" index="2"/> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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parents:
diff
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261 <column name="value" index="3"/> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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262 <column name="dbkey" index="1"/> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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parents:
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263 </options> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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264 </param> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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265 </when> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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266 |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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267 <when value="history_all"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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268 <param type="data" format="vcf" name="input" label="VCF file" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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269 <param type="data" format="csv" name="input_chain" multiple="false" label="LiftOver chain file" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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270 <param type="data" format="fasta" name="input_fasta" multiple="false" label="Full genome FASTA file" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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271 </when> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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272 </conditional> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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273 |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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274 <param name="include_fails" type="hidden" tvalue="False" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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275 </when> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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276 <when value="wig"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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277 <conditional name="seq_source"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
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278 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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279 <option value="cached">Local data (in galaxy)</option> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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280 <option value="history">From History</option> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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281 </param> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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282 <when value="cached"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
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diff
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283 <param format="wig" name="input" type="data" label="Wiggle file"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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|
284 <validator type="unspecified_build" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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285 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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|
286 </param> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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287 <param name="input_chain" type="select" label="Lift Over To"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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288 <options from_file="liftOver.loc"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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289 <column name="name" index="1"/> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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290 <column name="value" index="2"/> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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291 <column name="dbkey" index="0"/> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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292 <filter type="data_meta" ref="input" key="dbkey" column="0" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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293 </options> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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294 </param> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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295 </when> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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296 <when value="history"> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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297 <param format="wig" name="input" type="data" label="Wiggle file" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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298 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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299 </when> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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300 </conditional> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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|
301 |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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302 <param name="include_fails" type="hidden" tvalue="False" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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303 </when> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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304 </conditional> |
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bfcdabc062ca
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305 </inputs> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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306 |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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307 <outputs> |
|
6
5ef4ac8f2956
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 7ab6217b10b7483a03140eddc9c0567551b41b62
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5
diff
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308 <data format="text" name="output" label="${tool.name} on ${on_string}"> |
|
0
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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309 <change_format> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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310 <when input="multiple.input_format" value="bam" format="bam" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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311 <when input="multiple.input_format" value="sam" format="sam" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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312 <when input="multiple.input_format" value="bed" format="bed" /> |
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bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
313 <when input="multiple.input_format" value="bigwig" format="bigwig" /> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
314 <when input="multiple.input_format" value="gff" format="gff" /> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
315 <when input="multiple.input_format" value="vcf" format="vcf" /> |
|
6
5ef4ac8f2956
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 7ab6217b10b7483a03140eddc9c0567551b41b62
yhoogstrate
parents:
5
diff
changeset
|
316 <when input="multiple.input_format" value="wig" format="bigwig" /> |
|
0
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
317 </change_format> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
318 </data> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
319 |
|
6
5ef4ac8f2956
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 7ab6217b10b7483a03140eddc9c0567551b41b62
yhoogstrate
parents:
5
diff
changeset
|
320 <data format="text" name="output_unmapped" label="${tool.name} (unmapped) on ${on_string}"> |
|
5ef4ac8f2956
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 7ab6217b10b7483a03140eddc9c0567551b41b62
yhoogstrate
parents:
5
diff
changeset
|
321 <filter>multiple['input_format'] in ["bam" , "vcf"]</filter> |
|
0
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
322 <change_format> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
323 <when input="multiple.input_format" value="bam" format="bam" /> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
324 <when input="multiple.input_format" value="vcf" format="vcf" /> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
325 </change_format> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
326 </data> |
|
6
5ef4ac8f2956
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 7ab6217b10b7483a03140eddc9c0567551b41b62
yhoogstrate
parents:
5
diff
changeset
|
327 <data format="text" name="output2" label="${tool.name} (bedgraph) on ${on_string}"> |
|
5ef4ac8f2956
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 7ab6217b10b7483a03140eddc9c0567551b41b62
yhoogstrate
parents:
5
diff
changeset
|
328 <filter>multiple['input_format'] in ["wig"]</filter> |
|
0
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
329 <change_format> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
330 <when input="multiple.input_format" value="wig" format="bedgraph" /> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
331 </change_format> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
332 </data> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
333 </outputs> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
334 |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
335 <tests> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
336 <!-- BAM/SAM --> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
337 <test> |
|
7
1efce8a693ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
yhoogstrate
parents:
6
diff
changeset
|
338 <param name="input_format" value="bam"/> |
|
1efce8a693ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
yhoogstrate
parents:
6
diff
changeset
|
339 <param name="index_source" value="history"/> |
|
1efce8a693ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
yhoogstrate
parents:
6
diff
changeset
|
340 <param name="input" value="test_bam_01_input_a.sam" ftype="bam"/> |
|
1efce8a693ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
yhoogstrate
parents:
6
diff
changeset
|
341 <param name="input_chain" value="aToB.over.chain" ftype="csv"/> |
|
1efce8a693ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
yhoogstrate
parents:
6
diff
changeset
|
342 <param name="include_fails" value="False"/> |
|
1efce8a693ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
yhoogstrate
parents:
6
diff
changeset
|
343 |
|
1efce8a693ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
yhoogstrate
parents:
6
diff
changeset
|
344 <output name="output" file="test_bam_01_output_a.sam" compare="diff" lines_diff="4"/> |
|
1efce8a693ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
yhoogstrate
parents:
6
diff
changeset
|
345 <output name="output_unmapped" file="test_bam_01_output_a.unmap.sam"/> |
|
1efce8a693ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
yhoogstrate
parents:
6
diff
changeset
|
346 </test> |
|
1efce8a693ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
yhoogstrate
parents:
6
diff
changeset
|
347 |
|
1efce8a693ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
yhoogstrate
parents:
6
diff
changeset
|
348 <test> |
|
0
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
349 <param name="input_format" value="sam"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
350 <param name="index_source" value="history"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
351 <param name="input" value="test_bam_01_input_a.sam" ftype="sam"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
352 <param name="input_chain" value="aToB.over.chain" ftype="csv"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
353 <param name="include_fails" value="False"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
354 |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
355 <output name="output" file="test_bam_01_output_a.sam" compare="diff" lines_diff="4"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
356 <output name="output_unmapped" file="test_bam_01_output_a.unmap.sam"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
357 </test> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
358 |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
359 <!-- BED --> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
360 <test> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
361 <param name="input_format" value="bed"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
362 <param name="index_source" value="history"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
363 <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
364 <param name="input_chain" value="aToB.over.chain" ftype="csv"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
365 <param name="include_fails" value="False"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
366 |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
367 <output name="output" file="test_bed_01_output_a__only-matches.bed"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
368 </test> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
369 <test> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
370 <param name="input_format" value="bed"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
371 <param name="index_source" value="history"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
372 <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
373 <param name="input_chain" value="aToB.over.chain" ftype="txt"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
374 <param name="include_fails" value="True"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
375 |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
376 <output name="output" file="test_bed_01_output_a__all.bed"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
377 </test> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
378 <test> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
379 <param name="input_format" value="bed"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
380 <param name="index_source" value="history"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
381 <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
382 <param name="input_chain" value="aToB.over.chain" ftype="txt"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
383 <param name="include_fails" value="False"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
384 |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
385 <output name="output" file="test_bed_02_output_a__only-matches.bed"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
386 </test> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
387 <test> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
388 <param name="input_format" value="bed"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
389 <param name="index_source" value="history"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
390 <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
391 <param name="input_chain" value="aToB.over.chain" ftype="txt"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
392 <param name="include_fails" value="True"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
393 |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
394 <output name="output" file="test_bed_02_output_a__all.bed"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
395 </test> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
396 |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
397 <!-- BigWig --><!-- Malfuncioning in CrossMap 0.2, but patched via galaxy toolshed installer --> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
398 <test> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
399 <param name="input_format" value="bigwig"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
400 <param name="index_source" value="history"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
401 <param name="input" value="test_bigwig_01_input_a.bw" ftype="bigwig"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
402 <param name="input_chain" value="aToB.over.chain" ftype="csv"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
403 <param name="include_fails" value="False"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
404 |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
405 <output name="output" file="test_bigwig_01_output_a.bw"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
406 <output name="output2" file="test_bigwig_01_output_a.sorted.bgr"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
407 </test> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
408 <!-- GFF --> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
409 <test> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
410 <param name="input_format" value="gff"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
411 <param name="index_source" value="history"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
412 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
413 <param name="input_chain" value="aToB.over.chain" ftype="csv"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
414 <param name="include_fails" value="False"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
415 |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
416 <output name="output" file="test_gff_01_output_a__only-matches.gtf"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
417 </test> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
418 <test> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
419 <param name="input_format" value="gff"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
420 <param name="index_source" value="history"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
421 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
422 <param name="input_chain" value="aToB.over.chain" ftype="csv"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
423 <param name="include_fails" value="True"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
424 |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
425 <output name="output" file="test_gff_01_output_a__all.gtf"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
426 </test> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
427 |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
428 <!-- VCF --> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
429 <test> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
430 <param name="input_format" value="vcf"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
431 <param name="index_source" value="history_all"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
432 <param name="input" value="test_vcf_01_input.vcf" ftype="vcf"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
433 <param name="input_chain" value="test_vcf_01.over.chain" ftype="csv"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
434 <param name="input_fasta" value="test_vcf_01.fasta" ftype="fasta"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
435 <param name="include_fails" value="False"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
436 |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
437 <output name="output" file="test_vcf_01_output.vcf" compare="diff" lines_diff="4"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
438 <output name="output_unmapped" file="test_vcf_01_output.vcf.unmap"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
439 </test> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
440 </tests> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
441 |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
442 <!-- WIG - Doesn't understand fixedStep --> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
443 <test> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
444 <param name="input_format" value="wig"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
445 <param name="index_source" value="history"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
446 <param name="input" value="test_wig_01_input_a.wig" ftype="wig"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
447 <param name="input_chain" value="aToB.over.chain" ftype="csv"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
448 <param name="include_fails" value="False"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
449 |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
450 <output name="output" file="test_wig_01_output_a.bw"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
451 <output name="output2" file="test_wig_01_output_a.sorted.bgr"/> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
452 </test> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
453 <help> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
454 CrossMap is versatile tool to convert genome coordinates or annotation files between genome |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
455 assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF, |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
456 GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
457 and VCF, reading from remote servers and file compression are supported. |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
458 |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
459 CrossMap bed |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
460 ------------ |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
461 BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns. |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
462 BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
463 </help> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
464 |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
465 <citations> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
466 <citation type="doi">10.1093/bioinformatics/btt730</citation> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
467 </citations> |
|
bfcdabc062ca
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff
changeset
|
468 </tool> |