Mercurial > repos > agpetit > calculate_diameter
annotate calculate_diameter.xml @ 8:d45cecb7cfd0 draft
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
author | agpetit |
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date | Mon, 30 May 2022 15:56:59 +0000 |
parents | c574ada16e76 |
children | 066606280457 |
rev | line source |
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2
c574ada16e76
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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1 <tool id="calculate_diameter" name="calculate pore diameter of AQP" version="1.0.0" python_template_version="3.5" profile="@GALAXY_VERSION@" > |
1
658c6ec58e91
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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2 <macros> |
658c6ec58e91
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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3 <token name="@GALAXY_VERSION@">21.05</token> |
658c6ec58e91
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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4 </macros> |
0
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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5 <requirements> |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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6 <requirement type="package" version="2.1.0">mdanalysis</requirement> |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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7 </requirements> |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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8 <command detect_errors="exit_code"><![CDATA[ |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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9 python '$__tool_directory__/calculate_pore_diameter_aqp.py' |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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10 --arr_one '$arr1' |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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11 --arr_second '$arr2' |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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12 --gro_file '$gro_file' |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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13 --xtc_file '$xtc_file' |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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14 --gro_file_ext '$gro_file.ext' |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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15 --xtc_file_ext '$xtc_file.ext' |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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16 --output '$table' |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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17 --verbose |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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18 --log_output '$tool_log' |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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19 --output_directory 'out' |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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20 2>&1 |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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21 ]]></command> |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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22 <inputs> |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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23 <param name="gro_file" type="data" format="gro" optional="False" help="Put your .gro file"/> |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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24 <param name="xtc_file" type="data" format="xtc" optional="False" help="Put your .xtc file"/> |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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25 <param name="arr1" type="text" optional="False" label="pattern1" help="Pattern1 is a sequence of four amino acids. The first amino acid of this sequence will be the one used for the pore diameter of measurement. Example : HSD LEU ALA THR"> |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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26 <validator type="regex" message="Syntax error. 4 amino acids requested separated by a space.">^(ALA|CYS|ASP|GLU|PHE|GLY|HIS|ILE|LYS|LEU|MET|ASN|PRO|GLN|ARG|SER|THR|VAL|TRP|TYR|HSD|HSP)( (ALA|CYS|ASP|GLU|PHE|GLY|HIS|ILE|LYS|LEU|MET|ASN|PRO|GLN|ARG|SER|THR|VAL|TRP|TYR|HSD|HSP))( (ALA|CYS|ASP|GLU|PHE|GLY|HIS|ILE|LYS|LEU|MET|ASN|PRO|GLN|ARG|SER|THR|VAL|TRP|TYR|HSD|HSP))( (ALA|CYS|ASP|GLU|PHE|GLY|HIS|ILE|LYS|LEU|MET|ASN|PRO|GLN|ARG|SER|THR|VAL|TRP|TYR|HSD|HSP))*$</validator> |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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27 </param> |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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28 <param name="arr2" type="text" optional="False" label="pattern2" help="Pattern2 is a sequence of four amino acids. The first amino acid of this sequence will be the one used for the pore diameter of measurement. Example : ARG SER PHE GLY"> |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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29 <validator type="regex" message="Syntax error. 4 amino acids requested separated by a space.">^(ALA|CYS|ASP|GLU|PHE|GLY|HIS|ILE|LYS|LEU|MET|ASN|PRO|GLN|ARG|SER|THR|VAL|TRP|TYR|HSD|HSP)( (ALA|CYS|ASP|GLU|PHE|GLY|HIS|ILE|LYS|LEU|MET|ASN|PRO|GLN|ARG|SER|THR|VAL|TRP|TYR|HSD|HSP))( (ALA|CYS|ASP|GLU|PHE|GLY|HIS|ILE|LYS|LEU|MET|ASN|PRO|GLN|ARG|SER|THR|VAL|TRP|TYR|HSD|HSP))( (ALA|CYS|ASP|GLU|PHE|GLY|HIS|ILE|LYS|LEU|MET|ASN|PRO|GLN|ARG|SER|THR|VAL|TRP|TYR|HSD|HSP))*$</validator> |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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30 </param> |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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31 </inputs> |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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32 <outputs> |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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33 <data name="table" format="tabular" from_work_dir="out/" label="${tool.name} (Tabular)"/> |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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34 <data name="tool_log" format="txt" from_work_dir="out/*.log" label="${tool.name} (LOG)"/> |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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35 </outputs> |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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36 <tests> |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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37 <test> |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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38 <param name="gro_file" value="PIP2.1_test.gro" ftype="gro" /> |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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39 <param name="xtc_file" value="PIP2.1_test.xtc" ftype="xtc" /> |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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40 <param name="arr1" value="HSD LEU ALA THR"/> |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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41 <param name="arr2" value="ARG SER PHE GLY"/> |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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42 <output name="table" file="pair_dist_arr.tabular" /> |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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43 <output name="tool_log" file="calculate_pore_diameter_aqp.log" /> |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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44 </test> |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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45 </tests> |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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46 <help><![CDATA[ |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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47 |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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48 .. class:: infomark |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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49 |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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50 **What it does** |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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51 |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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52 This tool allows to launch a calculation of the pore diameter of an aquaporin as a function of time from a .gro file and an .xtc file. The calculation is made between the alpha carbons of two amino acids. |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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53 |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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54 _____ |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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55 |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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56 .. class:: infomark |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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57 |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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58 **Inputs** |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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59 |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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60 - gro_file : .gro file created with GROMACS containing the system coordinates. |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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61 - xtc_file : .xtc file created during a GROMACS simulation containing the trajectory for a given time of the system. |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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62 - pattern1 : a sequence of 4 amino acids. Each amino acid is named according to its 3-letter code. |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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63 - pattern2 : a sequence of 4 amino acids. Each amino acid is named according to its 3-letter code. |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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64 |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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65 _____ |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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66 |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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67 .. class:: infomark |
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"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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68 |
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"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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69 **Outputs** |
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"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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70 |
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"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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71 - TSV file : contains all the distance measurements on a part of the trajectory and the average of these distances. |
e227d80e53be
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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72 - LOG file of the tool execution |
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"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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73 |
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"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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74 ]]></help> |
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"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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75 <citations> |
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"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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76 <citation type="doi">10.1093/bioinformatics/btz107</citation> |
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"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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77 </citations> |
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"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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78 </tool> |