Anyone developing API scripts who likes to live dangerously - please read on.<div><br><div>I just tested and blend-lib api scripts work fine in Galaxy when pasted into a Tool Factory form. No need to generate a new tool.</div>
<div><br></div><div>Compared with running in a console, you get persistence and other framework benefits plus at no extra charge, a ginormous security problem if you share the history or any outputs because they contain the api script with key so development servers only please!</div>
<div> </div><div>Leave the input box empty, set the interpreter to python, paste and run an api script - eg working example (substitute the url and key) below.</div><div><div><br></div><div>Took me a few iterations to develop the example - after each run, the (edited..) api script is conveniently recreated using the redo button on the history output item. </div>
<div>So each successive version of the developing api script I ran was persisted - ready to be edited and rerun easily - handy being able to quickly inspect dicts to help move progressively deeper iteratively. </div><div>
<br></div><div><div>Give the below a whirl on a private clone (install the tool factory from the main toolshed) and try adding complexity with few rerun/edit/rerun cycles.</div><div><div><br></div><div>=============Eg tool factory api script=======================</div>
<div><br><div><div><div>import sys</div><div>from blend.galaxy import GalaxyInstance</div><div>ourGal = &#39;http://x.x.x.x:xxxx&#39;</div><div>ourKey = &#39;xxx&#39;</div><div>gi = GalaxyInstance(ourGal, key=ourKey)</div>
<div>libs = gi.libraries.get_libraries()</div><div>res = []</div><div>for lib in libs: #u&#39;url&#39;: u&#39;/galaxy/api/libraries/441d8112651dc2f3&#39;, u&#39;id&#39;: u&#39;441d8112651dc2f3&#39;, u&#39;name&#39;: u&#39;Demonstration sample RNA data&#39;, </div>
<div>    res.append(&#39;%s:\n&#39; % lib[&#39;name&#39;])</div><div>    res.append(str(gi.libraries.show_library(lib[&#39;id&#39;],contents=True)))</div><div>outf=open(sys.argv[2],&#39;w&#39;)</div><div>outf.write(&#39;\n&#39;.join(res))</div>
<div>outf.close()</div></div><div><br></div><div><br></div><div>returns a history item with:</div><div><br></div><div><table id="content_table" cellpadding="0" style="max-width:100%;border-collapse:collapse;color:rgb(48,48,48);font-family:&#39;Lucida Grande&#39;,verdana,arial,helvetica,sans-serif;font-size:12px;line-height:15px">
<tbody><tr><td class="stringalign" style="text-align:left;white-space:nowrap;padding-top:2px;padding-right:10px;padding-bottom:2px;padding-left:10px">Demonstration sample RNA data:</td></tr><tr><td class="stringalign" style="text-align:left;white-space:nowrap;padding-top:2px;padding-right:10px;padding-bottom:2px;padding-left:10px">
</td></tr><tr><td class="stringalign" style="text-align:left;white-space:nowrap;padding-top:2px;padding-right:10px;padding-bottom:2px;padding-left:10px">[{u&#39;url&#39;: u&#39;/galaxy/api/libraries/441d8112651dc2f3/contents/F8de0c7750d06c0d0&#39;, u&#39;type&#39;: u&#39;folder&#39;, u&#39;name&#39;: u&#39;/&#39;, u&#39;id&#39;: u&#39;F8de0c7750d06c0d0&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/441d8112651dc2f3/contents/F7d480bbb847db8d0&#39;, u&#39;type&#39;: u&#39;folder&#39;, u&#39;name&#39;: u&#39;/rnaseq demo data&#39;, u&#39;id&#39;: u&#39;F7d480bbb847db8d0&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/441d8112651dc2f3/contents/8b25a086f3d48921&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: u&#39;/rnaseq demo data/hg19_exons_mergedGENENAMES.bed&#39;, u&#39;id&#39;: u&#39;8b25a086f3d48921&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/441d8112651dc2f3/contents/5091b660e3557a3e&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: u&#39;/rnaseq demo data/Select first on Ctrl_HAEC_FC078_1_sequence.txt (data 1)&#39;, u&#39;id&#39;: u&#39;5091b660e3557a3e&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/441d8112651dc2f3/contents/4e084a2837e50c40&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: u&#39;/rnaseq demo data/Select first on Ctrl_HAEC_FC078_4_sequence.txt (data 4)&#39;, u&#39;id&#39;: u&#39;4e084a2837e50c40&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/441d8112651dc2f3/contents/0ab9ae3dbe24ad04&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: u&#39;/rnaseq demo data/Select first on Ctrl_HAEC_FC079_1_sequence.txt (data 7)&#39;, u&#39;id&#39;: u&#39;0ab9ae3dbe24ad04&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/441d8112651dc2f3/contents/0a773730795f59a9&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: u&#39;/rnaseq demo data/Select first on HG_HAEC_FC078_2_sequence.txt (data 2)&#39;, u&#39;id&#39;: u&#39;0a773730795f59a9&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/441d8112651dc2f3/contents/c810c4dc5aed60ac&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: u&#39;/rnaseq demo data/Select first on HG_HAEC_FC078_5_sequence.txt (data 5)&#39;, u&#39;id&#39;: u&#39;c810c4dc5aed60ac&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/441d8112651dc2f3/contents/ee5b8d53fd29c05c&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: u&#39;/rnaseq demo data/Select first on HG_HAEC_FC079_2_sequence.txt (data 8)&#39;, u&#39;id&#39;: u&#39;ee5b8d53fd29c05c&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/441d8112651dc2f3/contents/1e04e5f52ca2af6e&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: u&#39;/rnaseq demo data/Select first on HN_HAEC_FC078_3_sequence.txt (data 3)&#39;, u&#39;id&#39;: u&#39;1e04e5f52ca2af6e&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/441d8112651dc2f3/contents/7e05ba393ab04bc6&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: u&#39;/rnaseq demo data/Select first on HN_HAEC_FC078_6_sequence.txt (data 6)&#39;, u&#39;id&#39;: u&#39;7e05ba393ab04bc6&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/441d8112651dc2f3/contents/335753abc7341224&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: u&#39;/rnaseq demo data/Select first on HN_HAEC_FC079_3_sequence.txt (data 9)&#39;, u&#39;id&#39;: u&#39;335753abc7341224&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/441d8112651dc2f3/contents/09c975479974360d&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: u&#39;/smalltest.sam&#39;, u&#39;id&#39;: u&#39;09c975479974360d&#39;}]</td>
</tr><tr><td class="stringalign" style="text-align:left;white-space:nowrap;padding-top:2px;padding-right:10px;padding-bottom:2px;padding-left:10px">Public data:</td></tr><tr><td class="stringalign" style="text-align:left;white-space:nowrap;padding-top:2px;padding-right:10px;padding-bottom:2px;padding-left:10px">
</td></tr><tr><td class="stringalign" style="text-align:left;white-space:nowrap;padding-top:2px;padding-right:10px;padding-bottom:2px;padding-left:10px">[{u&#39;url&#39;: u&#39;/galaxy/api/libraries/37c082b4cb3811bd/contents/F37c082b4cb3811bd&#39;, u&#39;type&#39;: u&#39;folder&#39;, u&#39;name&#39;: u&#39;/&#39;, u&#39;id&#39;: u&#39;F37c082b4cb3811bd&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/37c082b4cb3811bd/contents/F5390d290c0aca35b&#39;, u&#39;type&#39;: u&#39;folder&#39;, u&#39;name&#39;: u&#39;/1000 genomes and other public fastq and bam samples&#39;, u&#39;id&#39;: u&#39;F5390d290c0aca35b&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/37c082b4cb3811bd/contents/721cc53ac555050e&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: u&#39;/1000 genomes and other public fastq and bam samples/<a href="ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA20351/sequence_read/SRR040058.filt.fastq">ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA20351/sequence_read/SRR040058.filt.fastq</a>&#39;, u&#39;id&#39;: u&#39;721cc53ac555050e&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/37c082b4cb3811bd/contents/a96ce863d2b9a69a&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: u&#39;/1000 genomes and other public fastq and bam samples/<a href="ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA20351/sequence_read/SRR040058.filt.fastq">ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA20351/sequence_read/SRR040058.filt.fastq</a> (data 10)_FastQC.html&#39;, u&#39;id&#39;: u&#39;a96ce863d2b9a69a&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/37c082b4cb3811bd/contents/81d4a112e7668435&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: u&#39;/1000 genomes and other public fastq and bam samples/1000g paired sample chr20&#39;, u&#39;id&#39;: u&#39;81d4a112e7668435&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/37c082b4cb3811bd/contents/00776454b8f394c8&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: u&#39;/1000 genomes and other public fastq and bam samples/1000g chrom 10 single QC sample&#39;, u&#39;id&#39;: u&#39;00776454b8f394c8&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/37c082b4cb3811bd/contents/0ff2a12d5b5e045a&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: u&#39;/1000 genomes and other public fastq and bam samples/1000g sample chr1 single ended reads&#39;, u&#39;id&#39;: u&#39;0ff2a12d5b5e045a&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/37c082b4cb3811bd/contents/8b394966390e7e29&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: u&#39;/1000 genomes and other public fastq and bam samples/Galaxy_GM12878.fastqillumina&#39;, u&#39;id&#39;: u&#39;8b394966390e7e29&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/37c082b4cb3811bd/contents/1b82079d07b4928f&#39;, u&#39;type&#39;: u&#39;file&#39;, 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u&#39;file&#39;, u&#39;name&#39;: u&#39;/rn5/rn5.fa&#39;, u&#39;id&#39;: u&#39;3afff7e53e7e8d39&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/37c082b4cb3811bd/contents/f0655257dc41a11e&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: u&#39;/rn5/rn5 refGene gtf august 21&#39;, u&#39;id&#39;: u&#39;f0655257dc41a11e&#39;}]</td>
</tr><tr><td class="stringalign" style="text-align:left;white-space:nowrap;padding-top:2px;padding-right:10px;padding-bottom:2px;padding-left:10px">Sample analyses and demonstration outputs:</td></tr><tr><td class="stringalign" style="text-align:left;white-space:nowrap;padding-top:2px;padding-right:10px;padding-bottom:2px;padding-left:10px">
</td></tr><tr><td class="stringalign" style="text-align:left;white-space:nowrap;padding-top:2px;padding-right:10px;padding-bottom:2px;padding-left:10px">[{u&#39;url&#39;: u&#39;/galaxy/api/libraries/b318d28ff7462b6a/contents/F50341ab0b3df0ae8&#39;, u&#39;type&#39;: u&#39;folder&#39;, u&#39;name&#39;: u&#39;/&#39;, u&#39;id&#39;: u&#39;F50341ab0b3df0ae8&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/b318d28ff7462b6a/contents/Ffb72a36640097dbe&#39;, u&#39;type&#39;: u&#39;folder&#39;, u&#39;name&#39;: u&#39;/qc demos&#39;, u&#39;id&#39;: u&#39;Ffb72a36640097dbe&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/b318d28ff7462b6a/contents/f5a85862afc5ed23&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: u&#39;/qc demos/Draw nucleotides distribution chart on data 5&#39;, u&#39;id&#39;: u&#39;f5a85862afc5ed23&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/b318d28ff7462b6a/contents/ff852b8d55f36ba4&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: u&#39;/qc demos/Draw quality score boxplot on data 5&#39;, u&#39;id&#39;: u&#39;ff852b8d55f36ba4&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/b318d28ff7462b6a/contents/7986d528d5b4a4a3&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: u&#39;/qc demos/FastQC demo.html&#39;, u&#39;id&#39;: u&#39;7986d528d5b4a4a3&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/b318d28ff7462b6a/contents/8332fcb92fd16073&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: u&#39;/qc demos/FC052_6_H3K4_me3_mock GC bias metrics.html&#39;, u&#39;id&#39;: u&#39;8332fcb92fd16073&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/b318d28ff7462b6a/contents/b40dd1185087841d&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: u&#39;/qc demos/Picard Alignment Summary Metrics demo.html&#39;, u&#39;id&#39;: u&#39;b40dd1185087841d&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/b318d28ff7462b6a/contents/cc1418787ba47d5b&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: u&#39;/qc demos/Short Read QC demo.html&#39;, u&#39;id&#39;: u&#39;cc1418787ba47d5b&#39;}]</td>
</tr><tr><td class="stringalign" style="text-align:left;white-space:nowrap;padding-top:2px;padding-right:10px;padding-bottom:2px;padding-left:10px">Cardiac_Hypertrophy_mRNA-seq:</td></tr><tr><td class="stringalign" style="text-align:left;white-space:nowrap;padding-top:2px;padding-right:10px;padding-bottom:2px;padding-left:10px">
</td></tr><tr><td class="stringalign" style="text-align:left;white-space:nowrap;padding-top:2px;padding-right:10px;padding-bottom:2px;padding-left:10px">[{u&#39;url&#39;: u&#39;/galaxy/api/libraries/177c1b293cbb701a/contents/F40ab8504ce94ef0d&#39;, u&#39;type&#39;: u&#39;folder&#39;, u&#39;name&#39;: u&#39;/&#39;, u&#39;id&#39;: u&#39;F40ab8504ce94ef0d&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/177c1b293cbb701a/contents/0f0d4fbd4c36508e&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: u&#39;/FC080_7_sequence.txt&#39;, u&#39;id&#39;: u&#39;0f0d4fbd4c36508e&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/177c1b293cbb701a/contents/4379f92c040d9d38&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: u&#39;/FC080_8_sequence.txt&#39;, u&#39;id&#39;: u&#39;4379f92c040d9d38&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/177c1b293cbb701a/contents/5e2ec5e41af06eff&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: u&#39;/FC081_7_sequence.txt&#39;, u&#39;id&#39;: u&#39;5e2ec5e41af06eff&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/177c1b293cbb701a/contents/437508e7c34a0e88&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: u&#39;/FC081_8_sequence.txt&#39;, u&#39;id&#39;: u&#39;437508e7c34a0e88&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/177c1b293cbb701a/contents/9c7e2377b7fbc18c&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: u&#39;/FC083_1_sequence.txt&#39;, u&#39;id&#39;: u&#39;9c7e2377b7fbc18c&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/177c1b293cbb701a/contents/37b691840fb310fe&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: u&#39;/FC083_2_sequence.txt&#39;, u&#39;id&#39;: u&#39;37b691840fb310fe&#39;}]</td>
</tr><tr><td class="stringalign" style="text-align:left;white-space:nowrap;padding-top:2px;padding-right:10px;padding-bottom:2px;padding-left:10px">New data library:</td></tr><tr><td class="stringalign" style="text-align:left;white-space:nowrap;padding-top:2px;padding-right:10px;padding-bottom:2px;padding-left:10px">
</td></tr><tr><td class="stringalign" style="text-align:left;white-space:nowrap;padding-top:2px;padding-right:10px;padding-bottom:2px;padding-left:10px">[{u&#39;url&#39;: u&#39;/galaxy/api/libraries/d49c9ce6b21e26bc/contents/F4cf130617fab4439&#39;, u&#39;type&#39;: u&#39;folder&#39;, u&#39;name&#39;: u&#39;/&#39;, u&#39;id&#39;: u&#39;F4cf130617fab4439&#39;}]</td>
</tr><tr><td class="stringalign" style="text-align:left;white-space:nowrap;padding-top:2px;padding-right:10px;padding-bottom:2px;padding-left:10px">BakerIDI Short Read Data:</td></tr><tr><td class="stringalign" style="text-align:left;white-space:nowrap;padding-top:2px;padding-right:10px;padding-bottom:2px;padding-left:10px">
</td></tr><tr><td class="stringalign" style="text-align:left;white-space:nowrap;padding-top:2px;padding-right:10px;padding-bottom:2px;padding-left:10px">[{u&#39;url&#39;: u&#39;/galaxy/api/libraries/6cd82b8eed63ee9a/contents/F6dd4fb50f5ab1620&#39;, u&#39;type&#39;: u&#39;folder&#39;, u&#39;name&#39;: u&#39;/&#39;, u&#39;id&#39;: u&#39;F6dd4fb50f5ab1620&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/6cd82b8eed63ee9a/contents/F1368058342340557&#39;, u&#39;type&#39;: u&#39;folder&#39;, u&#39;name&#39;: u&#39;/AngII_Raelene&#39;, u&#39;id&#39;: u&#39;F1368058342340557&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/6cd82b8eed63ee9a/contents/a9733d836b4b719c&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: u&#39;/AngII_Raelene/Ang_CpG_high_cat_merged_peaks.mx&#39;, u&#39;id&#39;: u&#39;a9733d836b4b719c&#39;}, {u&#39;url&#39;: u&#39;/galaxy/api/libraries/6cd82b8eed63ee9a/contents/03d82016c24dc39a&#39;, u&#39;type&#39;: u&#39;file&#39;, u&#39;name&#39;: 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