Mercurial > repos > devteam > sam_to_bam
annotate sam_to_bam.xml @ 9:d83ad701f011 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
author | iuc |
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date | Sat, 27 Nov 2021 12:27:56 +0000 |
parents | c701f5f96f32 |
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rev | line source |
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c701f5f96f32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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1 <tool id="sam_to_bam" name="SAM-to-BAM" version="2.1.2" profile="@PROFILE@"> |
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4afb4a5f0924
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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2 <description>convert SAM to BAM</description> |
4afb4a5f0924
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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3 |
4afb4a5f0924
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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4 <macros> |
4afb4a5f0924
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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5 <import>macros.xml</import> |
4afb4a5f0924
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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6 </macros> |
4afb4a5f0924
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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7 <expand macro="requirements"/> |
4afb4a5f0924
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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8 <expand macro="stdio"/> |
4afb4a5f0924
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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9 <expand macro="version_command"/> |
4afb4a5f0924
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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10 |
4afb4a5f0924
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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11 <command><![CDATA[ |
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c701f5f96f32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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12 @ADDTHREADS@ |
c701f5f96f32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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13 @ADDMEMORY@ |
c701f5f96f32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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14 @PREPARE_FASTA_IDX@ |
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4afb4a5f0924
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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15 |
4afb4a5f0924
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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16 samtools view |
4afb4a5f0924
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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17 -b |
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c701f5f96f32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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18 -@ \$addthreads |
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d83ad701f011
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
iuc
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19 -t "\$reffai" |
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c701f5f96f32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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20 '$input' | |
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4afb4a5f0924
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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21 |
4afb4a5f0924
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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22 samtools sort |
4afb4a5f0924
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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23 -O bam |
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c701f5f96f32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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24 -@ \$addthreads -m \$addmemory"M" |
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4afb4a5f0924
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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25 -o '$output1' |
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a832dc88e7dc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"
iuc
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26 -T "\${TMPDIR:-.}" |
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4afb4a5f0924
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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27 ]]></command> |
4afb4a5f0924
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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28 |
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5a5f92086188
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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29 <inputs> |
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c701f5f96f32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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30 <param name="input" type="data" format="sam" label="SAM file to convert"/> |
c701f5f96f32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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31 <expand macro="mandatory_reference" argument="-t"/> |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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32 </inputs> |
5a5f92086188
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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33 <outputs> |
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4afb4a5f0924
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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34 <data name="output1" format="bam" label="${tool.name} on ${on_string}: converted BAM"> |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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35 <actions> |
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c701f5f96f32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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36 <conditional name="addref_cond.addref_select"> |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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37 <when value="cached"> |
5a5f92086188
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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38 <action name="dbkey" type="metadata"> |
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c701f5f96f32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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39 <option name="input" param_attribute="dbkey" type="from_param" /> |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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40 </action> |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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41 </when> |
5a5f92086188
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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42 <when value="history"> |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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43 <action name="dbkey" type="metadata"> |
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c701f5f96f32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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44 <option name="addref_cond.ref" param_attribute="dbkey" type="from_param" /> |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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45 </action> |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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46 </when> |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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47 </conditional> |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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48 </actions> |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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49 </data> |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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50 </outputs> |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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51 <tests> |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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52 <test> |
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c701f5f96f32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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53 <param name="addref_select" value="history" /> |
c701f5f96f32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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54 <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" /> |
c701f5f96f32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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55 <param name="input" ftype="sam" value="sam_to_bam_in1.sam" /> |
c701f5f96f32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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56 <output name="output1" ftype="bam" file="sam_to_bam_out1.bam" lines_diff="4"/> |
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4afb4a5f0924
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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57 </test> |
4afb4a5f0924
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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58 <test> |
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c701f5f96f32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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59 <param name="addref_select" value="cached" /> |
c701f5f96f32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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60 <param name="ref" value="equCab2chrM" /> |
c701f5f96f32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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61 <param name="input" ftype="sam" dbkey="equCab2" value="sam_to_bam_in1.sam" /> |
c701f5f96f32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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62 <output name="output1" ftype="bam" file="sam_to_bam_out2.bam" lines_diff="4"/> |
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63 </test> |
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64 <test> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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65 <param name="addref_select" value="history" /> |
c701f5f96f32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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66 <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" /> |
c701f5f96f32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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67 <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" /> |
c701f5f96f32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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68 <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/> |
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69 </test> |
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d83ad701f011
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
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70 <test> |
d83ad701f011
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
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71 <!-- Test direct use of bgzipped reference --> |
d83ad701f011
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
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72 <param name="addref_select" value="history" /> |
d83ad701f011
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
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73 <param name="ref" ftype="fasta.gz" dbkey="equCab2" value="chr_m.bgzipped_fasta.gz" /> |
d83ad701f011
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
iuc
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74 <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" /> |
d83ad701f011
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
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75 <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/> |
d83ad701f011
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
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76 </test> |
d83ad701f011
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
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77 <test> |
d83ad701f011
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
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78 <!-- Test with simple gzipped reference, which requires decompression --> |
d83ad701f011
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
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79 <param name="addref_select" value="history" /> |
d83ad701f011
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
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80 <param name="ref" ftype="fasta.gz" dbkey="equCab2" value="chr_m.fasta.gz" /> |
d83ad701f011
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
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81 <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" /> |
d83ad701f011
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
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82 <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/> |
d83ad701f011
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
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83 </test> |
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84 </tests> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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85 <help><![CDATA[ |
0 | 86 **What it does** |
87 | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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88 Converts SAM dataset into its binary, BAM, representation using the ``samtools view`` and ``sort`` commands. |
4afb4a5f0924
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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89 ]]></help> |
4afb4a5f0924
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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90 <expand macro="citations"/> |
0 | 91 </tool> |