Mercurial > repos > iuc > kallisto_pseudo
annotate kallisto_pseudo.xml @ 2:1c75aa5de15e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
author | iuc |
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date | Sat, 09 Dec 2017 05:34:01 -0500 |
parents | 2953303df011 |
children | 5ae5c312d718 |
rev | line source |
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0
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
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1 <?xml version="1.0"?> |
2
1c75aa5de15e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
iuc
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0
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2 <tool id="kallisto_pseudo" name="Kallisto pseudo" version="@VERSION@.1"> |
0
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
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3 <description>- run pseudoalignment on RNA-Seq transcripts</description> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
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4 <macros> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
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5 <import>macros.xml</import> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
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6 </macros> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
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7 <expand macro="requirements" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
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8 <command detect_errors="exit_code"> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
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9 <![CDATA[ |
2
1c75aa5de15e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
iuc
parents:
0
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10 #if $reference_transcriptome.reference_transcriptome_source == "history": |
1c75aa5de15e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
iuc
parents:
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11 ln -s '$reference_transcriptome.reference' reference.fa && |
0
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
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12 kallisto index reference.fa -i reference.kallisto && |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
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13 #set index_path = 'reference.kallisto' |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
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14 #else: |
2
1c75aa5de15e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
iuc
parents:
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15 #set index_path = $reference_transcriptome.index.fields.path |
0
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
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16 #end if |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
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17 kallisto pseudo -i '$index_path' |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
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18 #if $pseudobam: |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
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19 $pseudobam -o . |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
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20 #else: |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
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21 --threads \${GALAXY_SLOTS:-1} |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
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22 -o . |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
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23 #end if |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
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24 |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
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25 |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
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26 #if str($single_paired.single_paired_selector) == 'single': |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
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27 --single --fragment-length $single_paired.fragment_length |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
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28 --sd $single_paired.sd '$single_paired.reads' |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
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29 #else: |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
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30 #if str($single_paired.collection.collection_selector) == 'collection': |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
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31 '$single_paired.collection.reads.forward' |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
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32 '$single_paired.collection.reads.reverse' |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
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33 #else: |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
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34 #if str($single_paired.collection.fastq_umi.umi) == 'yes': |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
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35 --batch '$batch' --umi |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
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36 #else: |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
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37 '$single_paired.collection.fastq_umi.forward' |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
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38 '$single_paired.collection.fastq_umi.reverse' |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
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39 #end if |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
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40 #end if |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
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41 #end if |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
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42 #if $pseudobam: |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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43 | samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -o '$pseudobam_output' - |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
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44 #end if |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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45 && if [ -f run_info.json ] ; then cat run_info.json ; fi && |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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46 mkdir outputs && |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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47 if [ -f matrix.ec ] ; then mv matrix.ec outputs/Matrix.ec ; fi && |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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48 if [ -f matrix.tsv ] ; then mv matrix.tsv outputs/Matrix.tabular ; fi && |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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49 if [ -f matrix.cells ] ; then mv matrix.cells outputs/Matrix.cells ; fi && |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
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50 if [ -f pseudoalignments.tsv ] ; then mv pseudoalignments.tsv outputs/Pseudoalignments.tabular ; fi && |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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51 if [ -f pseudoalignments.ec ] ; then mv pseudoalignments.ec outputs/Pseudoalignments.ec ; fi |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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52 ]]> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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53 </command> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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54 <configfiles> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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55 <configfile name="batch"> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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56 <![CDATA[ |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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57 #if str($single_paired.single_paired_selector) == 'single': |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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58 cell1 $single_paired.reads |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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59 #else: |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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60 #if str($single_paired.collection.collection_selector) == 'collection': |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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61 cell1 $single_paired.collection.reads.forward $single_paired.collection.reads.reverse |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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62 #else: |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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63 cell1 $single_paired.collection.fastq_umi.forward $single_paired.collection.fastq_umi.reverse |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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64 #end if |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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65 #end if |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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66 ]]> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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67 </configfile> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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68 </configfiles> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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69 <inputs> |
2
1c75aa5de15e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
iuc
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70 <expand macro="reference_input" /> |
0
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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71 <conditional name="single_paired"> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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72 <param name="single_paired_selector" type="select" label="Single-end or paired reads"> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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73 <option value="single" selected="true">Single-end</option> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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74 <option value="paired">Paired</option> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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75 </param> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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76 <when value="single"> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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77 <param name="reads" type="data" format="fastq" multiple="True" label="Reads in FASTQ format" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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78 <param name="fragment_length" argument="--fragment-length" type="integer" value="200" label="Average fragment length" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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79 <param argument="--sd" type="integer" value="20" label="Estimated standard deviation of fragment length" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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80 </when> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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81 <when value="paired"> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
|
82 <conditional name="collection"> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
|
83 <param name="collection_selector" type="select" label="Collection or individual datasets"> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
|
84 <option value="datasets" selected="true">Individual files</option> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
|
85 <option value="collection">Pair or list of pairs</option> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
|
86 </param> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
|
87 <when value="datasets"> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
|
88 <conditional name="fastq_umi"> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
|
89 <param name="umi" type="select" label="Pseudoalignment uses UMIs"> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
|
90 <option value="no" selected="true">Paired FASTQ</option> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
|
91 <option value="yes">UMI</option> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
|
92 </param> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
|
93 <when value="yes"> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
|
94 <param name="forward" type="data" format="tabular" multiple="True" label="UMI file" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
diff
changeset
|
95 <param name="reverse" type="data" format="fastq" multiple="True" label="FASTQ reads" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
parents:
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changeset
|
96 </when> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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diff
changeset
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97 <when value="no"> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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98 <param name="forward" type="data" format="fastq" multiple="True" label="Forward reads" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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99 <param name="reverse" type="data" format="fastq" multiple="True" label="Reverse reads" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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changeset
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100 </when> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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101 </conditional> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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changeset
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102 </when> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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103 <when value="collection"> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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104 <param name="reads" type="data_collection" format="fastq" collection_type="paired" label="Collection of reads" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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changeset
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105 </when> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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106 </conditional> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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changeset
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107 </when> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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108 </conditional> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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109 <param argument="--pseudobam" type="boolean" truevalue="--pseudobam" falsevalue="" label="Output pseudoalignments in BAM format" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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110 </inputs> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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111 <outputs> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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112 <data format="tabular" name="sample"> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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113 <discover_datasets pattern="(?P<designation>.+)" directory="outputs" ext="tabular" visible="true" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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114 </data> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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115 <data format="bam" name="pseudobam_output" label="${tool.name} on ${on_string}: Pseudoalignments (BAM)"> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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116 <filter>pseudobam</filter> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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117 </data> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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118 </outputs> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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119 <tests> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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120 <test> |
2
1c75aa5de15e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
iuc
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0
diff
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121 <param name="reference_transcriptome_source" value="history" /> |
0
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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122 <param name="reference" ftype="fasta" value="mm10_chrM.fa" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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123 <param name="single_paired_selector" value="paired" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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124 <param name="collection_selector" value="datasets" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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125 <param name="umi" value="yes" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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126 <param name="forward" ftype="tabular" value="mm10_chrM.umi" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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127 <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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128 <output name="sample"> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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129 <discovered_dataset designation="Matrix.tabular" file="kallisto_pseudo_out1.tab" ftype="tabular" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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130 <discovered_dataset designation="Matrix.ec" file="kallisto_pseudo_out1.ec" ftype="tabular" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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131 <discovered_dataset designation="Matrix.cells" file="kallisto_pseudo_out1.cells" ftype="tabular" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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132 </output> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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133 </test> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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134 <test> |
2
1c75aa5de15e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
iuc
parents:
0
diff
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135 <param name="reference_transcriptome_source" value="history" /> |
0
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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136 <param name="reference" ftype="fasta" value="mm10_chrM.fa" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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137 <param name="single_paired_selector" value="paired" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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138 <param name="collection_selector" value="collection" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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139 <param name="umi" value="no" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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140 <param name="reads"> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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141 <collection type="paired"> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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142 <element name="forward" value="mm10_chrM-1.f.fq" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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143 <element name="reverse" value="mm10_chrM-1.r.fq" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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144 </collection> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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145 </param> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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146 <output name="sample"> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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147 <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out2.tab" ftype="tabular" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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148 <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out2.ec" ftype="tabular" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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149 </output> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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150 </test> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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151 <test> |
2
1c75aa5de15e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
iuc
parents:
0
diff
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152 <param name="reference_transcriptome_source" value="history" /> |
0
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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153 <param name="reference" ftype="fasta" value="mm10_chrM.fa" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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154 <param name="single_paired_selector" value="single" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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155 <param name="collection_selector" value="collection" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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156 <param name="reads" ftype="fastq" value="mm10_chrM-1.f.fq" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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157 <output name="sample"> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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158 <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out3.tab" ftype="tabular" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
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159 <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out3.ec" ftype="tabular" /> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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160 </output> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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161 </test> |
2953303df011
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
iuc
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162 <test> |
2
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163 <param name="reference_transcriptome_source" value="history" /> |
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164 <param name="reference" ftype="fasta" value="felCat8_chrM.fa" /> |
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165 <param name="single_paired_selector" value="paired" /> |
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166 <param name="collection_selector" value="datasets" /> |
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167 <param name="umi" value="no" /> |
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168 <param name="forward" ftype="fastq" value="felCat8_chrM_F.fq" /> |
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169 <param name="reverse" ftype="fastq" value="felCat8_chrM_R.fq" /> |
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170 <output name="sample"> |
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171 <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out4.tab" ftype="tabular" /> |
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172 <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out4.ec" ftype="tabular" /> |
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173 </output> |
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174 </test> |
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175 <test> |
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176 <param name="reference_transcriptome_source" value="cached" /> |
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177 <param name="single_paired_selector" value="paired" /> |
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178 <param name="collection_selector" value="datasets" /> |
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179 <param name="pseudobam" value="true" /> |
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180 <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_F.fq.gz" /> |
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181 <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" /> |
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182 <output name="sample"> |
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183 <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out5.tab" ftype="tabular" /> |
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184 <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out5.ec" ftype="tabular" /> |
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185 </output> |
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186 <output name="pseudobam_output" file="kallisto_pseudo_out5.bam" ftype="bam" /> |
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187 </test> |
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188 <test> |
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189 <param name="reference_transcriptome_source" value="cached" /> |
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190 <param name="single_paired_selector" value="paired" /> |
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191 <param name="collection_selector" value="datasets" /> |
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192 <param name="umi" value="yes" /> |
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193 <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM.umi" /> |
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194 <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" /> |
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195 <output name="sample"> |
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196 <discovered_dataset designation="Matrix.tabular" file="kallisto_pseudo_out6.tab" ftype="tabular" /> |
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197 <discovered_dataset designation="Matrix.ec" file="kallisto_pseudo_out6.ec" ftype="tabular" /> |
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198 <discovered_dataset designation="Matrix.cells" file="kallisto_pseudo_out6.cells" ftype="tabular" /> |
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199 </output> |
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200 </test> |
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201 </tests> |
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202 <help> |
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203 <![CDATA[ |
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204 `kallisto <https://pachterlab.github.io/kallisto/manual>`__ is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. |
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205 ]]> |
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206 </help> |
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207 <expand macro="citations" /> |
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208 </tool> |