Mercurial > repos > ebi-gxa > scanpy_run_umap

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Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
author ebi-gxa
date Tue, 27 Feb 2024 16:42:43 +0000
parents 9984f48961d0
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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1 <macros>
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ea91cfd0444e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
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2 <token name="@TOOL_VERSION@">1.9.3</token>
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0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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3 <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token>
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ea91cfd0444e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
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4 <token name="@PROFILE@">20.09</token>
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0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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5 <token name="@VERSION_HISTORY@"><![CDATA[
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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6 **Version history**
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ea91cfd0444e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
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7 1.9.301+galaxy0: Moves to Scanpy 1.9.3
ea91cfd0444e planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
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bd4a244faeb8 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6c9d530aa653101e9e21804393ec11f38cddf027-dirty
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9 1.8.1+galaxy9: Fixes version label to get versions sorted properly on Galaxy (equivalent to 1.8.1+3+galaxy0). In addition, adds ability to make fields unique in AnnData operations,
bd4a244faeb8 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6c9d530aa653101e9e21804393ec11f38cddf027-dirty
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10 adds additional handler on Scrubblet for workflows convenience, enables Scanpy tools to avoid outputing AnnData/matrix files when not required.
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0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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0f98603d0116 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9ea121884e1aecd2ee66a0686057cb3ed904b9eb-dirty"
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12 1.8.1+3+galaxy0: Upate to scanpy-scripts 1.1.3 (running scanpy ==1.8.1), including a fix to MTX output and a bugfix for the Scrublet wrapper.
0f98603d0116 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9ea121884e1aecd2ee66a0686057cb3ed904b9eb-dirty"
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ad70b3552c99 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 85dcbc74a856bd55865bd372601de39af72dfd29-dirty"
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14 1.8.1+2+galaxy0: Upate to scanpy-scripts 1.1.2 (running scanpy ==1.8.1), including improved boolean handling for mito etc.
ad70b3552c99 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 85dcbc74a856bd55865bd372601de39af72dfd29-dirty"
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ad70b3552c99 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 85dcbc74a856bd55865bd372601de39af72dfd29-dirty"
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16 1.8.1+1+galaxy0: Upate to scanpy-scripts 1.1.1 build 1 (running scanpy ==1.8.1), including improved Scrublet integration with batch handling.
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767a675b5254 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit cecd3663ae841b026216f01003d58ea7c3bfde3e-dirty"
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fe562424a0a6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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18 1.8.1+galaxy0: Upate to scanpy-scripts 1.0.1 (running scanpy ==1.8.1), including Scrublet integration.
fe562424a0a6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"
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3a7b97ddf3ff "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 858a2398f1dbbd60110867c593c237358c794615-dirty"
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20 1.7.2+galaxy0: Upate to scanpy-scripts 0.3.3 (running scanpy ==1.7.2) to incorporate fix for object output from PAGA plotting, to allow PAGA init of FDG.
3a7b97ddf3ff "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 858a2398f1dbbd60110867c593c237358c794615-dirty"
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f53bb2c1fa07 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"
ebi-gxa
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22 1.6.0+galaxy0: Update to scanpy-scripts 0.2.13 (running scanpy ==1.6.0) to incorporate new options, code simplifications, and batch integration methods. Jonathan Manning, Expression Atlas team https://www.ebi.ac.uk/gxa/home at
f53bb2c1fa07 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"
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23 EMBL-EBI https://www.ebi.ac.uk/
f53bb2c1fa07 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"
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b282c349bd67 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit edcca4677d954001b33ad15e22603ea452031d76
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25 1.4.3+galaxy10: Update to scanpy-scripts 0.2.10 (running scanpy ==1.4.3) to address bugfixes in run-pca.
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41f6078040da planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit cbe12e02ee9ff5692be7547bdbe28fd1cd013a92
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b282c349bd67 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit edcca4677d954001b33ad15e22603ea452031d76
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27 1.4.3+galaxy10: Update to scanpy-scripts 0.2.9 (running scanpy ==1.4.3) to address bugfixes in find-variable-genes.
b282c349bd67 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit edcca4677d954001b33ad15e22603ea452031d76
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b282c349bd67 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit edcca4677d954001b33ad15e22603ea452031d76
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29 1.4.3+galaxy10: Use profile 18.01 for modules.
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aa85725f43a2 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit d52bedbcef249117567014584058429525883ef7-dirty
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6eb7a2e37adf planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 400799f99ee36ad12b990b1ccabf4be16a26c003
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31 1.4.3+galaxy6: Update to scanpy-scripts 0.2.8 (running scanpy ==1.4.3) and wider compatibility with other Galaxy modules. Bug fixes in filtering and plotting improvements.
6eb7a2e37adf planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 400799f99ee36ad12b990b1ccabf4be16a26c003
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01750c193a83 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ccd9b839849600b1aa3b6cf54f667575a5f2da9d
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33 1.4.3+galaxy0: Update to scanpy-scripts 0.2.5 (running scanpy ==1.4.3).
01750c193a83 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ccd9b839849600b1aa3b6cf54f667575a5f2da9d
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0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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35 1.4.2+galaxy0: Update to scanpy-scripts 0.2.4 (requires scanpy >=1.4.2).
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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37 1.3.2+galaxy1: Normalise-data and filter-genes: Exposes ability to output 10x files.
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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39 1.3.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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40 EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute.
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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41 ]]></token>
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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42 <token name="@INPUT_OPTS@">
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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43 --input-format '${input_format}' input.h5
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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44 </token>
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e31937baa330 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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45 <token name="@SAVE_MATRIX_OPTS@">
e31937baa330 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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46 #if $save_raw
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47 --save-raw
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48 #end if
e31937baa330 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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49 #if $save_layer
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50 --save-layer ${save_layer}
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e31937baa330 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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51 #end if
e31937baa330 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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52 </token>
1
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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53 <token name="@OUTPUT_OPTS@">
5
6eb7a2e37adf planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 400799f99ee36ad12b990b1ccabf4be16a26c003
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54 #if str($output_format).startswith('anndata')
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55 --show-obj stdout --output-format anndata output.h5
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56 #else
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57 --show-obj stdout --output-format loom output.h5
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58 #end if
1
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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59 </token>
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60 <token name="@PLOT_OPTS@">
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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61 #if $fig_title
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62 --title '${fig_title}'
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63 #end if
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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64 --fig-size '${fig_size}'
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65 --fig-dpi ${fig_dpi}
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66 --fig-fontsize ${fig_fontsize}
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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67 ${fig_frame}
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68 ./output.png
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69 </token>
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70 <token name="@EXPORT_MTX_OPTS@">${export_mtx}</token>
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71
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72 <xml name="requirements">
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73 <requirements>
27
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74 <requirement type="package" version="1.9.301">scanpy-scripts</requirement>
1
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75 <yield/>
27
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76 <!-- use this format when you want to test against provisional conda artifacts
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77 <container type="docker">quay.io/biocontainers/scanpy-scripts:1.9.301 pyhdfd78af_0</container>
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78 -->
1
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79 </requirements>
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80 </xml>
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81
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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82 <xml name="citations">
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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83 <citations>
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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84 <yield />
27
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85 <citation type="doi">10.1038/s41592-021-01102-w</citation>
1
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86 <citation type="doi">10.1186/s13059-017-1382-0</citation>
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87 <citation type="bibtex">
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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88 @misc{githubscanpy-scripts,
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89 author = {Ni Huang, EBI Gene Expression Team},
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90 year = {2018},
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91 title = {Scanpy-scripts: command line interface for Scanpy},
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92 publisher = {GitHub},
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93 journal = {GitHub repository},
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94 url = {https://github.com/ebi-gene-expression-group/scanpy-scripts},
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95 }</citation>
11
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96 <citation type="doi">10.1101/2020.04.08.032698</citation>
1
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97 </citations>
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98 </xml>
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99
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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100 <xml name="input_object_params">
5
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101 <param name="input_obj_file" argument="input-object-file" type="data" format="h5,h5ad" label="Input object in AnnData/Loom format"/>
1
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102 <param name="input_format" argument="--input-format" type="select" label="Format of input object">
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103 <option value="anndata" selected="true">AnnData format hdf5</option>
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104 <option value="loom">Loom format hdf5</option>
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105 </param>
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106 </xml>
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107
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108 <xml name="output_object_params">
25
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109 <param name="output_format" argument="--output-format" type="select" label="Format of output object" help="AnnData or Loom. Legacy 'h5' datatypes are useful for interacting with older tools. Choosing 'No packaged matrix output' is useful for cases where auxiliary files are generated (like in marker genes). Do not use when there are no other output files, as the tool will generate no output in Galaxy then.">
5
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110 <option value="anndata_h5ad" selected="true">AnnData format</option>
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111 <option value="anndata">AnnData format (h5 for older versions)</option>
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112 <option value="loom">Loom format</option>
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113 <option value="loom_legacy">Loom format (h5 for older versions)</option>
25
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114 <option value="no_matrix_output">No packaged matrix output</option>
5
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115 </param>
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116 </xml>
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117
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118 <xml name="output_object_params_no_loom">
25
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119 <param name="output_format" argument="--output-format" type="select" label="Format of output object" help="Legacy 'h5' datatypes are useful for interacting with older tools. Choosing 'No packaged matrix output' is useful for cases where auxiliary files are generated (like in marker genes). Do not use when there are no other output files, as the tool will generate no output in Galaxy then.">
5
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120 <option value="anndata_h5ad" selected="true">AnnData format</option>
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121 <option value="anndata">AnnData format (h5 for older versions)</option>
25
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122 <option value="no_matrix_output">No packaged matrix output (useful for cases where auxiliary files are generated)</option>
1
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123 </param>
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124 </xml>
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125
5
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126 <xml name="output_data_obj_no_loom" token_description="operation">
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127 <data name="output_h5ad" format="h5ad" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
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128 <filter>output_format == 'anndata_h5ad'</filter>
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129 </data>
25
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130 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData (h5)">
5
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131 <filter>output_format == 'anndata'</filter>
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132 </data>
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133 </xml>
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134
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135 <xml name="output_data_obj" token_description="operation">
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136 <data name="output_h5ad" format="h5ad" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
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137 <filter>output_format == 'anndata_h5ad'</filter>
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138 </data>
25
bd4a244faeb8 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6c9d530aa653101e9e21804393ec11f38cddf027-dirty
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139 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData (h5)">
5
6eb7a2e37adf planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 400799f99ee36ad12b990b1ccabf4be16a26c003
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140 <filter>output_format == 'anndata'</filter>
6eb7a2e37adf planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 400799f99ee36ad12b990b1ccabf4be16a26c003
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141 </data>
6eb7a2e37adf planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 400799f99ee36ad12b990b1ccabf4be16a26c003
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142 <data name="output_loom_legacy" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ Loom">
6eb7a2e37adf planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 400799f99ee36ad12b990b1ccabf4be16a26c003
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143 <filter>output_format == 'loom_legacy'</filter>
6eb7a2e37adf planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 400799f99ee36ad12b990b1ccabf4be16a26c003
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144 </data>
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bd4a244faeb8 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6c9d530aa653101e9e21804393ec11f38cddf027-dirty
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145 <data name="output_loom" format="loom" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ Loom (h5)">
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6eb7a2e37adf planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 400799f99ee36ad12b990b1ccabf4be16a26c003
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146 <filter>output_format == 'loom'</filter>
6eb7a2e37adf planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 400799f99ee36ad12b990b1ccabf4be16a26c003
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147 </data>
6eb7a2e37adf planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 400799f99ee36ad12b990b1ccabf4be16a26c003
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148 </xml>
6eb7a2e37adf planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 400799f99ee36ad12b990b1ccabf4be16a26c003
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149
19
e31937baa330 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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150 <xml name="save_matrix_params">
e31937baa330 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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151 <param name="save_raw" argument="--save-raw" type="boolean" truevalue="yes" falsevalue="no" checked="false"
e31937baa330 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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152 label="Save adata to adata.raw before processing?" />
e31937baa330 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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153 <param name="save_layer" argument="--save-layer" type="text" optional="true"
e31937baa330 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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154 label="Save adata.X to the specified layer before processing."/>
e31937baa330 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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155 </xml>
e31937baa330 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
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156
1
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157 <xml name="output_plot_params">
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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158 <param name="fig_title" argument="--title" type="text" label="Figure title"/>
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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159 <param name="fig_size" argument="--fig-size" type="text" value="4,4" label="Figure size as 'width,height', e.g, '7,7'"/>
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160 <param name="fig_dpi" argument="--fig-dpi" type="integer" min="1" value="80" label="Figure dpi"/>
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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161 <param name="fig_fontsize" argument="--fig-fontsize" type="integer" min="0" value="10" label="Figure font size"/>
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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162 <param name="fig_frame" type="boolean" truevalue="--frameon" falsevalue="--frameoff" checked="false"
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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163 label="Show plot frame"/>
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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164 </xml>
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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165
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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166 <xml name="export_mtx_params">
3
c111d7d04f0b planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit d13a0a5fceabe51e1a6fe763767b963623aa295a
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167 <param name="export_mtx" argument="--export-mtx" type="boolean" truevalue="--export-mtx ./" falsevalue="" checked="false" label="Save to 10x mtx format" help="If enabled, it will generate in addition to the main output in Loom or AnnData an export in 10x format."/>
1
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168 </xml>
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169
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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170 <xml name="export_mtx_outputs">
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171 <data name="matrix_10x" format="txt" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string}: 10x matrix">
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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172 <filter>export_mtx</filter>
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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173 </data>
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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174 <data name="genes_10x" format="tsv" from_work_dir="genes.tsv" label="${tool.name} on ${on_string}: 10x genes">
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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175 <filter>export_mtx</filter>
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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176 </data>
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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177 <data name="barcodes_10x" format="tsv" from_work_dir="barcodes.tsv" label="${tool.name} on ${on_string}: 10x barcodes">
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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178 <filter>export_mtx</filter>
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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179 </data>
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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180 </xml>
0ac2f9f2313b "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"
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181 </macros>